Methods and systems for multiplex quantitative nucleic acid amplification

ABSTRACT

The present disclosure provides methods, devices and systems that enable simultaneous multiplexing amplification reaction and real-time detection in a single reaction chamber.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No.14/850,659, filed Sep. 10, 2015 all of which is herein incorporated byreference in its entirety.

BACKGROUND

Nucleic acid target amplification assays such as polymerase chainreaction process (PCR) can amplify (i.e., replicate) specific sequencesof nucleic acids of a DNA template in-vitro. The target amplificationassays may become a powerful and widely-used tool in molecular biologyand genomics, as they can selectively increase the number of copies oftarget molecules from a just a few to billions in a matter of hours andthus making the targets easily detectable. While, in most cases, suchamplification and subsequent detection are typically done for one targetnucleic molecule per reaction volume, it is of great interest toefficiently multiplex the assays in the same reaction volume and allowfor multiple concurrent target amplification and detection in the samereaction chamber. Such an approach may not only better utilize the“precious” original DNA sample, but also significantly reduce anycomplexities associated with the fluidics and liquid-handling proceduresfor running multiple single-plex reactions.

SUMMARY

Recognized herein are various issues with currently availablemultiplexed PCR methods. For instance, while multiplexing a large numberof target amplification reactions (e.g., multiplexed PCR) may bepossible, it is not straightforward to detect multiple ampliconssimultaneously. So far, multiplexed Q-PCR methods, defined as theprocesses by which one amplifies and detects a plurality of nucleic acidsequences simultaneously in a single reaction chamber, has beenimplemented for a small number of amplicons, generally less than ten.Accordingly, recognized herein is a need for methods and systems thatenable multiplex nucleic acid amplification and real-time quantitativedetection.

The present disclosure provides methods, devices and systems foramplifying a plurality of nucleic acid sequences and real-timemonitoring the amplification processes and evaluating quantitatively thegenerated products, in a single reaction chamber.

An aspect of the present disclosure provides a method for assaying apresence or absence of at least one target nucleic acid molecule,comprising: (a) providing a reaction mixture comprising a nucleic acidsample suspected of containing the at least one template nucleic acidmolecule, a primer pair and a polymerase, wherein the primer pair hassequence complementarity with the template nucleic acid molecule, andwherein the primer pair comprises a limiting primer and an excessprimer; (b) subjecting the reaction mixture to a nucleic acidamplification reaction under conditions that yield the at least onetarget nucleic acid molecule as an amplification product of the templatenucleic acid molecule; (c) bringing the reaction mixture in contact witha sensor array having (i) a substrate comprising a plurality of probesimmobilized to a surface of the substrate at different individuallyaddressable locations, wherein the probes are capable of capturing thetarget nucleic acid molecule and/or the limiting primer, and (ii) anarray of detectors configured to detect at least one signal from theaddressable locations, wherein the at least one signal is indicative ofthe presence or absence of the target nucleic acid molecule and/or thelimiting primer; (d) using the array of detectors to detect the at leastone signal from one or more the addressable locations at multiple timepoints during the nucleic acid amplification reaction; and (e)identifying the presence or absence of the target nucleic acid moleculeand/or the limiting primer based on the at least one signal.

In some embodiments of aspects provided herein, the at least one signalis produced upon binding of the probes to the target nucleic acidmolecule and/or the limiting primer. In some embodiments of aspectsprovided herein, the reaction mixture comprises a plurality of templatenucleic acid molecules and the probes specifically bind to a pluralityof target nucleic molecules as amplification products of the pluralityof template nucleic acid molecules. In some embodiments of aspectsprovided herein, the reaction mixture comprises a plurality of limitingprimers having different nucleic acid sequences, and the probesspecifically bind to the plurality of the limiting primers. In someembodiments of aspects provided herein, the reaction mixture is providedin a reaction chamber configured to retain the reaction mixture andpermit the probes to bind to the target nucleic acid molecule and/or thelimiting primer. In some embodiments of aspects provided herein, themethod further comprises correlating the detected at least one signal atmultiple time points with an original concentration of the at least onetemplate nucleic acid molecule by analyzing a binding rate of the probeswith the target nucleic acid molecule or the limiting primer. In someembodiments of aspects provided herein, the probes are oligonucleotides.In some embodiments of aspects provided herein, the target nucleic acidmolecule forms a hairpin loop when hybridized to an individual probe. Insome embodiments of aspects provided herein, the sensor array comprisesat least about 100 integrated sensors, at least about 500 integratedsensors, at least about 1,000 integrated sensors, at least about 2,000integrated sensors, at least about 5,000 integrated sensors or at leastabout 10,000 integrated sensors. In some embodiments of aspects providedherein, the at least one signal is an optical signal that is indicativeof an interaction between an energy acceptor and an energy donor. Insome embodiments of aspects provided herein, the energy acceptorquenches optical activity of the energy donor. In some embodiments ofaspects provided herein, the energy acceptor is coupled to the excessprimer and/or the limiting primer. In some embodiments of aspectsprovided herein, the energy acceptor is coupled to the target nucleicacid molecule. In some embodiments of aspects provided herein, theenergy acceptor is a quencher. In some embodiments of aspects providedherein, the energy donor is a fluorophore. In some embodiments ofaspects provided herein, the at least one signal is an optical signalindicative of the activity of an optically-active species. In someembodiments of aspects provided herein, the optically-active species isan intercalator. In some embodiments of aspects provided herein, theoptically-active species is a fluorophore. In some embodiments ofaspects provided herein, the at least one signal is an electrical signalthat is indicative of an interaction between an electrode and a redoxlabel. In some embodiments of aspects provided herein, the redox labelis coupled to the excess primer and/or the limiting primer. In someembodiments of aspects provided herein, the redox label is coupled tothe target nucleic acid molecule. In some embodiments of aspectsprovided herein, (d) comprises measuring an increase in the at least onesignal relative to background. In some embodiments of aspects providedherein, (d) comprises measuring a decrease in the at least one signalrelative to background. In some embodiments of aspects provided herein,the sensor array comprises at least one optical detector that detectsthe at least one signal. In some embodiments of aspects provided herein,the optical detector comprises a complementary metal-oxide semiconductor(CMOS) device. In some embodiments of aspects provided herein, thesensor array comprises at least one electrical detector that detects theat least one signal. In some embodiments of aspects provided herein, theelectrical detector comprises a complementary metal-oxide semiconductor(CMOS) device. In some embodiments of aspects provided herein, theprobes are immobilized to the surface via a linker. In some embodimentsof aspects provided herein, the linker comprises a species selected fromthe group consisting of an amino acid, a polypeptide, a nucleotide andan oligonucleotide. In some embodiments of aspects provided herein, thetarget nucleic acid molecule is detected at a sensitivity of at leastabout 90%, at least about 95%, at least about 98%, at least about 99%,at least about 99.9%, or at least about 99.99%. In some embodiments ofaspects provided herein, the at least one signal is detected while thereaction mixture comprising the target nucleic acid molecule is in fluidcontact with the sensor array. In some embodiments of aspects providedherein, the method further comprises detecting at least one controlsignal from the sensor array. In some embodiments of aspects providedherein, the at least one signal is detected in real-time.

Another aspect of the present disclosure provides a method for assayinga presence or absence of at least one target nucleic acid molecule,comprising: (a) providing a reaction mixture comprising a nucleic acidsample, a primer pair, a polymerase and a nucleotide labeled with areporter molecule, wherein the nucleic acid sample is suspected ofcontaining the at least one template nucleic acid molecule, and whereinthe primer pair has sequence complementarity with the template nucleicacid molecule; (b) subjecting the reaction mixture to a nucleic acidamplification reaction under conditions that yield the at least onetarget nucleic acid molecule as an amplification product of the templatenucleic acid molecule, which nucleic acid amplification reactionincorporates the nucleotide into the template nucleic acid molecule; (c)bringing the reaction mixture in contact with a sensor array comprising(i) a substrate comprising a plurality of probes immobilized to asurface of the substrate at different individually addressablelocations, wherein the probes are capable of capturing the targetnucleic acid molecule, and (ii) an array of detectors configured todetect at least one signal from the addressable locations uponinteraction between the reporter molecule and at least one of theprobes, wherein the at least one signal is indicative of the presence orabsence of the target nucleic acid molecule; (d) using the array ofdetectors to detect the at least one signal from one or more theaddressable locations at multiple time points during the nucleic acidamplification reaction; and (e) identifying the presence or absence ofthe target nucleic acid molecule based on the at least one signal.

In some embodiments of aspects provided herein, the at least one signalis produced upon binding of the probes to the target nucleic acidmolecule comprising the reporter molecule. In some embodiments ofaspects provided herein, the reaction mixture is provided in a reactionchamber configured to retain the reaction mixture and permit the probesto bind to the target nucleic acid molecule. In some embodiments ofaspects provided herein, the nucleotide is deoxyribonucleotidetriphosphate (dNTP). In some embodiments of aspects provided herein, theprobes are oligonucleotides. In some embodiments of aspects providedherein, the target nucleic acid molecule forms a hairpin loop whenhybridized to an individual probe. In some embodiments of aspectsprovided herein, the sensor array comprises at least about 100integrated sensors, at least about 500 integrated sensors, at leastabout 1,000 integrated sensors, at least about 2,000 integrated sensors,at least about 5,000 integrated sensors or at least about 10,000integrated sensors. In some embodiments of aspects provided herein, thereporter molecule is an energy acceptor. In some embodiments of aspectsprovided herein, the at least one signal is an optical signal that isindicative of an interaction between the energy acceptor and an energydonor. In some embodiments of aspects provided herein, the energyacceptor quenches optical activity of the energy donor. In someembodiments of aspects provided herein, the energy acceptor is aquencher. In some embodiments of aspects provided herein, the energydonor is a fluorophore. In some embodiments of aspects provided herein,the at least one signal is an optical signal indicative of the activityof an optically-active species. In some embodiments of aspects providedherein, the optically-active species is an intercalator. In someembodiments of aspects provided herein, the optically-active species isa fluorophore. In some embodiments of aspects provided herein, thereporter molecule is a redox label. In some embodiments of aspectsprovided herein, the at least one signal is an electrical signal that isindicative of an interaction between an electrode and the redox label.In some embodiments of aspects provided herein, (d) comprises measuringan increase in the at least one signal relative to background. In someembodiments of aspects provided herein, (d) comprises measuring adecrease in the at least one signal relative to background. In someembodiments of aspects provided herein, the sensor array comprises anoptical detector that detects the at least one signal. In someembodiments of aspects provided herein, the optical detector comprises acomplementary metal-oxide semiconductor (CMOS) device. In someembodiments of aspects provided herein, the sensor array comprises anelectrical detector that detects the at least one signal. In someembodiments of aspects provided herein, the electrical detectorcomprises a complementary metal-oxide semiconductor (CMOS) device. Insome embodiments of aspects provided herein, the probes are immobilizedto the surface via a linker. In some embodiments of aspects providedherein, the linker comprises a species selected from the groupconsisting of an amino acid, a polypeptide, a nucleotide and anoligonucleotide. In some embodiments of aspects provided herein, thetarget nucleic acid molecule is detected as a sensitivity of at leastabout 90%, at least about 95%, at least about 98%, at least about 99%,at least about 99.9%, or at least about 99.99%. In some embodiments ofaspects provided herein, the method further comprises detecting at leastone control signal from the sensor array. In some embodiments of aspectsprovided herein, the at least one signal is detected in real-time. Insome embodiments of aspects provided herein, the reporter molecule is aquencher. In some embodiments of aspects provided herein, the probes arelabeled with fluorophores. In some embodiments of aspects providedherein, the reporter molecule is a fluorophore. In some embodiments ofaspects provided herein, the probes are labeled with quenchers. In someembodiments of aspects provided herein, the at least one signal isindicative of an interaction between the quencher and a given one of thefluorophores.

Another aspect of the present disclosure provides a system for assayinga presence or absence of at least one target nucleic acid molecule,comprising: (a) a reaction chamber configured to (i) retain a reactionmixture comprising a nucleic acid sample suspected of containing the atleast one template nucleic acid molecule, a primer pair that hassequence complementary to the template nucleic acid molecule, and apolymerase, wherein the primer pair comprises a limiting primer and anexcess primer, and (ii) facilitate a nucleic acid amplification reactionon the reaction mixture to yield at least one target nucleic acidmolecule as an amplification product of the template nucleic acid; (b) asensor array comprising (i) a substrate comprising a plurality of probesimmobilized to a surface of the substrate at different individuallyaddressable locations, wherein the probes are capable of capturing thetarget nucleic acid molecule and/or the limiting primer; and (ii) anarray of detectors configured to detect at least one signal from theaddressable locations, wherein the at least one signal is indicative ofa presence or absence of the target nucleic acid molecule and/or thelimiting primer; and (c) a computer processor coupled to the sensorarray and programmed to (i) subject the reaction mixture to the nucleicacid amplification reaction, and (ii) detect the at least one signalfrom one or more of the addressable locations at multiple time pointsduring the nucleic acid amplification reaction. In some embodiments ofaspects provided herein, the computer processor is programmed to detectthe at least one signal while the reaction mixture comprising the targetnucleic acid molecule is in fluid contact with the sensor array. In someembodiments of aspects provided herein, the computer processor isprogrammed to detect the at least one signal in real-time. In someembodiments of aspects provided herein, the sensor array comprises anoptical detector that is capable of detecting the at least one signal.In some embodiments of aspects provided herein, the optical detectorcomprises a complementary metal-oxide semiconductor (CMOS) device. Insome embodiments of aspects provided herein, the sensor array comprisesan electrical detector that is capable of detecting the at least onesignal. In some embodiments of aspects provided herein, the electricaldetector comprises a complementary metal-oxide semiconductor (CMOS)device. In some embodiments of aspects provided herein, the sensor arraycomprises at least about 100 integrated sensors, at least about 500integrated sensors, at least about 1000 integrated sensors, at leastabout 2000 integrated sensors, at least about 5000 integrated sensors orat least about 10,000 integrated sensors. In some embodiments of aspectsprovided herein, the computer processor is programmed to identify thepresence or absence of the target nucleic acid molecule and/or thelimiting primer based on the at least one signal.

Another aspect of the present disclosure provides a system for assayinga presence or absence of at least one target nucleic acid molecule,comprising: (a) a reaction chamber configured to (i) retain a reactionmixture comprising a nucleic acid sample suspected of containing the atleast one template nucleic acid molecule, a primer pair that hassequence complementary to the template nucleic acid molecule, apolymerase, and a nucleotide labeled with a reporter molecule, and (ii)facilitate a nucleic acid amplification reaction on the reaction mixtureto yield at least one target nucleic acid molecule as an amplificationproduct of the template nucleic acid, which nucleic acid amplificationreaction incorporates the nucleotide into the template nucleic acidmolecule; (b) a sensor array comprising (i) a substrate comprising aplurality of probes immobilized to a surface of the substrate atdifferent individually addressable locations, wherein the probes arecapable of capturing the target nucleic acid molecule, and (ii) an arrayof detectors configured to detect at least one signal from theaddressable locations upon interaction between the reporter molecule andat least one of the probes, wherein the at least one signal isindicative of the presence or absence of the target nucleic acidmolecule; and (c) a computer processor coupled to the sensor array andprogrammed to (i) subject the reaction mixture to the nucleic acidamplification reaction, and (ii) detect the at least one signal from theaddressable locations at multiple time points during the nucleic acidamplification reaction.

In some embodiments of aspects provided herein, the computer processoris programmed to detect the at least one signal while the reactionmixture comprising the target nucleic acid molecule is in fluid contactwith the sensor array. In some embodiments of aspects provided herein,the computer processor is programmed to detect the at least one signalin real-time. In some embodiments of aspects provided herein, the sensorarray comprises an optical detector that is capable of detecting the atleast one signal. In some embodiments of aspects provided herein, theoptical detector comprises a complementary metal-oxide semiconductor(CMOS) device. In some embodiments of aspects provided herein, thesensor array comprises an electrical detector that is capable ofdetecting the at least one signal. In some embodiments of aspectsprovided herein, the electrical detector comprises a complementarymetal-oxide semiconductor (CMOS) device. In some embodiments of aspectsprovided herein, the sensor array comprises at least about 100integrated sensors, at least about 500 integrated sensors, at leastabout 1000 integrated sensors, at least about 2000 integrated sensors,at least about 5000 integrated sensors or at least about 10,000integrated sensors. In some embodiments of aspects provided herein, thecomputer processor is programmed to identify the presence or absence ofthe target nucleic acid molecule based on the at least one signal.

Additional aspects and advantages of the present disclosure will becomereadily apparent to those skilled in this art from the followingdetailed description, wherein only illustrative embodiments of thepresent disclosure are shown and described. As will be realized, thepresent disclosure is capable of other and different embodiments, andits several details are capable of modifications in various obviousrespects, all without departing from the disclosure. Accordingly, thedrawings and description are to be regarded as illustrative in nature,and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings (also “figure” and “FIG.” herein), of which:

FIG. 1 schematically illustrates an example multiplex amplification anddetection system;

FIG. 2 schematically illustrates an example optical detection methodcomprising primer labeling;

FIG. 3 schematically illustrates an example optical detection methodcomprising non-labeled amplicons;

FIG. 4 schematically illustrated an example optical detection methodcomprising acceptor-labeled deoxynucleotide triphosphates (dNTPs);

FIG. 5 schematically illustrates an example electrical detection methodcomprising primer labeling;

FIG. 6 schematically illustrates an example electrical detection methodcomprising non-labeled amplicons;

FIG. 7 schematically illustrated an example electrical detection methodcomprising redox-labeled deoxynucleotide triphosphates (dNTPs);

FIG. 8 shows concentration of primers and amplicons in an exampleasymmetric PCR amplification and a conventional PCR amplificationmethods;

FIGS. 9A-9D show signals measured and threshold cycle (CO identified inan example asymmetric PCR amplification and a conventional PCRamplification methods;

FIG. 10 shows example images and a schematic of an optical biochipdetector;

FIG. 11 shows an example optical biochip circuit architecture;

FIG. 12 shows example images and a schematic of an electrical biochipdetector;

FIG. 13 shows an example electrical biochip circuit architecture;

FIGS. 14A-14C show an example method of detecting on-chip PCRamplification;

FIG. 15 shows example primer-complement and control-complementsequences;

FIG. 16 shows data measured in an example array;

FIG. 17 shows amplification data measured in an example array;

FIG. 18 shows signal measured in an example array; and

FIG. 19 shows an example computer control system that is programmed orotherwise configured to implement methods provided herein.

DETAILED DESCRIPTION

While various embodiments of the invention have been shown and describedherein, it will be obvious to those skilled in the art that suchembodiments are provided by way of example only. Numerous variations,changes, and substitutions may occur to those skilled in the art withoutdeparting from the invention. It should be understood that variousalternatives to the embodiments of the invention described herein may beemployed.

The term “quantitative-PCR” or “Q-PCR,” as used herein generally refersto a polymerase chain reaction (PCR) process that can be used for thequalitative and quantitative determination of nucleic acid sequences. Insome cases, Q-PCR is synonymous with real-time PCR. Q-PCR can involvethe measurement of the amount of amplification product (or amplicon) asa function of amplification cycle, and use such information to determinethe amount of the nucleic acid sequence corresponding to the ampliconthat was present in the original sample.

The term “probe” as used herein generally refers to a molecular speciesor other marker that can bind to a specific target nucleic acidsequence. A probe can be any type of molecule or particle. Probes cancomprise molecules and can be bound to the substrate or other solidsurface, directly or via a linker molecule.

The term “detector” as used herein generally refers to a device,generally including optical and/or electronic components that can detectsignals.

The term “mutation” as used herein generally refers to genetic mutationsor sequence variations such as a point mutation, a single nucleotidepolymorphism (SNP), an insertion, a deletion, a substitution, atransposition, a translocation, a copy number variation, or anothergenetic mutation, alteration or sequence variation.

The term “about” or “nearly” as used herein generally refers to within+/−15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% of the designatedamount.

The term “label” as used herein refers to a specific molecular structurethat can be attached to a target molecule, to make the target moleculedistinguishable and traceable by providing a unique characteristic notintrinsic to the target molecule.

The term “limiting,” as used herein in the context of a chemical orbiological reaction, generally refers to a species that is in a limitingamount (e.g., stoichiometrically limiting) in a given reaction volumesuch that upon completion of the chemical or biological reaction (e.g.,PCR), the species may not be present in the reaction volume.

The term “excess,” as used herein in the context of a chemical orbiological reaction, generally refers to a species that is in an excessamount (e.g., stoichiometrically limiting) in a given reaction volumesuch that upon completion of the chemical or biological reaction (e.g.,PCR), the species may be present in the reaction volume.

The term “nucleotide,” as used herein, generally refers a molecule thatcan serve as the monomer, or subunit, of a nucleic acid, such asdeoxyribonucleic acid (DNA) or ribonucleic acid RNA). A nucleotide canbe a deoxynucleotide triphosphate (dNTP) or an analog thereof, e.g., amolecule having a plurality of phosphates in a phosphate chain, such as2, 3, 4, 5, 6, 7, 8, 9, or 10 phosphates. A nucleotide can generallyinclude adenosine (A), cytosine (C), guanine (G), thymine (T) and uracil(U), or variants thereof. A nucleotide can include any subunit that canbe incorporated into a growing nucleic acid strand. Such subunit can bean A, C, G, T, or U, or any other subunit that is specific to one ormore complementary A, C, G, T or U, or complementary to a purine (i.e.,A or G, or variant thereof) or a pyrimidine (i.e., C, T or U, or variantthereof). A subunit can enable individual nucleic acid bases or groupsof bases (e.g., AA, TA, AT, GC, CG, CT, TC, GT, TG, AC, CA, oruracil-counterparts thereof) to be resolved. A nucleotide may be labeledor unlabeled. A labeled nucleotide may yield a detectable signal, suchas an optical, electrostatic or electrochemical signal.

A Q-PCR process can be described in the following non-limiting example.A PCR reaction is carried out with a pair of primers designed to amplifya given nucleic acid sequence in a sample. The appropriate enzymes andnucleotides, such as deoxynucleotide triphosphates (dNTPs), are added tothe reaction, and the reaction is subjected to a number of amplificationcycles. The amount of amplicon generated from each cycle is detected,but in the early cycles, the amount of amplicon can be below thedetection threshold. The amplification may be occurring in two phases,an exponential phase, followed by a non-exponential plateau phase.During the exponential phase, the amount of PCR product approximatelydoubles in each cycle. As the reaction proceeds, however, reactioncomponents are consumed, and ultimately one or more of the componentsbecomes limiting. At this point, the reaction slows and enters theplateau phase. Initially, the amount of amplicon remains at or belowbackground levels, and increases are not detectable, even thoughamplicon product accumulates exponentially. Eventually, enough amplifiedproduct accumulates to yield a detectable signal. The cycle number atwhich this occurs is called the threshold cycle, or C_(t). Since theC_(t) value is measured in the exponential phase when reagents are notlimited, Q-PCR can be used to reliably and accurately calculate theinitial amount of template present in the reaction. The C_(t) of areaction may be determined mainly by the amount of nucleic acid sequencecorresponding to amplicon present at the start of the amplificationreaction. If a large amount of template is present at the start of thereaction, relatively few amplification cycles may be required toaccumulate enough products to give a signal above background. Thus, thereaction may have a low, or early, C_(t). In contrast, if a small amountof template is present at the start of the reaction, more amplificationcycles may be required for the fluorescent signal to rise abovebackground. Thus, the reaction may have a high, or late, C_(t). Methodsand systems provided herein allow for the measurement of theaccumulation of multiple amplicons in a single fluid in a singleamplification reaction, and thus the determination of the amount ofmultiple nucleic acid sequences in the same sample with the methodologyof Q-PCR described above.

As used herein in, the term “real-time” generally refers to measuringthe status of a reaction while it is occurring, either in the transientphase or in biochemical equilibrium. Real-time measurements areperformed contemporaneously with the monitored, measured, or observedongoing events, as opposed to measurements taken after a reaction isfixed. Thus, a “real time” assay or measurement generally contains notonly the measured and quantitated result, such as fluorescence, butexpresses this at various time points, that is, in nanoseconds,microseconds, milliseconds, seconds, minutes, hours, etc. “Real-time”may include detection of the kinetic production of signal, comprisingtaking a plurality of readings in order to characterize the signal overa period of time. For example, a real-time measurement can comprise thedetermination of the rate of increase or decrease in the amount of ananalyte. While the measurement of signal in real-time can be useful fordetermining rate by measuring a change in the signal, in some cases themeasurement of no change in signal can also be useful. For example, thelack of change of a signal over time can be an indication that areaction (e.g., binding, hybridization) has reached a steady-state.

As used herein, the terms “polynucleotide”, “oligonucleotide”,“nucleotide”, “nucleic acid” and “nucleic acid molecule” generally referto a polymeric form of nucleotides (polynucleotides) of various lengths(e.g., 20 bases to 5000 kilo-bases), either ribonucleotides (RNA) ordeoxyribonucleotides (DNA). This term may refer only to the primarystructure of the molecule. Thus, the term may include triple-, double-and single-stranded DNA, as well as triple-, double- and single-strandedRNA. It may also include modifications, such as by methylation and/or bycapping, and unmodified forms of the polynucleotide.

Nucleic acids can comprise phosphodiester bonds (i.e. natural nucleicacids). Nucleic acids can comprise nucleic acid analogs that may havealternate backbones, comprising, for example, phosphoramide (see, e.g.,Beaucage et al., Tetrahedron 49(10):1925 (1993) and U.S. Pat. No.5,644,048), phosphorodithioate (see, e.g., Briu et al., J. Am. Chem.Soc. 11 1:2321 (1989), O-methylphosphoroamidite linkages (see, e.g.,Eckstein, Oligonucleotides and Analogues: A Practical Approach, OxfordUniversity Press), and peptide nucleic acid (PNA) backbones and linkages(see, e.g., Carlsson et al., Nature 380:207 (1996)). Nucleic acids cancomprise other analog nucleic acids including those with positivebackbones (see, e.g., Denpcy et al., Proc. Natl. Acad. Sci. USA 92:6097(1995); non-ionic backbones (see, e.g., U.S. Pat. Nos. 5,386,023,5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew.Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem.Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597(1994); Chapters 2 and 3, ASC Symposium Series 580, “CarbohydrateModifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook;Mesmaeker et al., Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffset al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743(1996)) and non-ribose backbones, (see, e.g., U.S. Pat. Nos. 5,235,033and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580,“Carbohydrate Modifications in Antisense Research”, Ed. Y. S. Sanghuiand P. Dan Cook). Nucleic acids can comprise one or more carbocyclicsugars (see, e.g., Jenkins et al., Chem. Soc. Rev. (1995) pp 169-176).These modifications of the ribose-phosphate backbone can facilitate theaddition of labels, or increase the stability and half-life of suchmolecules in physiological environments.

As used herein, the term “amplicon” generally refers to a molecularspecies that is generated from the amplification of a nucleotidesequence, such as through PCR. An amplicon may be a polynucleotide suchas RNA or DNA or mixtures thereof, in which the sequence of nucleotidesin the amplicon may correlate with the sequence of the nucleotidesequence from which it was generated (i.e. either corresponding to orcomplimentary to the sequence). The amplicon can be either singlestranded or double stranded. In some cases, the amplicon may begenerated by using one or more primers that is incorporated into theamplicon. In some cases, the amplicon may be generated in a polymerasechain reaction or PCR amplification, wherein two primers may be used toproduce either a pair of complementary single stranded amplicons or adouble-stranded amplicon.

As used herein, the term “probe” generally refers to a molecular speciesor a marker that can bind to a nucleic acid sequence. A probe can be anytype of molecules or particles. Probes can comprise molecules and can bebound to a substrate or a surface, directly or via a linker molecule.

As used herein, the singular forms “a”, “an”, and “the” include pluralreferences unless the context clearly dictates otherwise.

Overview

Quantification of amplicons during amplification processes, to enableQ-PCR, may be done based on measuring the light intensity or spectralpattern (e.g., frequency, frequency distribution or intensitydistribution) emanating from fluorescent reporter molecules that havesignal intensity associated with the generated PCR products. Themeasured light intensity in these processes may be used as an indicationof the actual number of the amplified sequences and the amplificationprocess. Some of the used methods, in single-plex PCR or otheramplification processes, may comprise intercalator fluorophore dyes thatcan bind to double-stranded DNA (dsDNA) such as SYBR Green or shortmodified DNA sequences in the form of hybridization or TaqMan probes.

Attempts at creating multiplex Q-PCR methods have been plagued bypractical issues of simultaneously detecting different nucleic acidsequences in a single sample. A possible approach is to associatedifferent reporter molecules (e.g., fluorescent dyes) to individualamplicons during the PCR reaction which may enable parallel detection ofindividual reporters by different “colors”. While such approach, intheory, may offer parallelism, is limited by (i) the number of differentreporter molecules available; and (ii) the availability of imagers anddetectors capable of differentiating different signals. Current Q-PCRsystems may be able to detect up to ten amplicons by using up to tendifferent fluorescent reporters. Another possible approach to offermultiplexing capability is to divide the biological sample of interestand physically place it, using fluidic systems, into separate, singleand isolated amplification chambers. While this approach may effectivelycreate multiplex Q-PCR by performing multiple single-plex (i.e., oneamplicon per chamber) Q-PCR reactions, it may be suboptimal, since itmay reduce the number of nucleic acid target sequences in each chamberwhich may create stochastic anomalies (Poisson noise) in the acquireddata when the original sample has a small concentration. Further, itrequires complex fluidic handling procedures.

Highly-multiplexed detection of DNA sequences in a sample may be donethrough adopting analytical platforms such as DNA microarrays or nextgeneration DNA sequencers, but not Q-PCR or equivalent. Microarrays, inparticular, are massively-parallel affinity-based biosensor wherenucleic acid targets are captured selectively from the same sample atdifferent addressable coordinates (e.g., pixels) on a solid surface.Each addressable coordinate can have a unique capturing DNA or RNAprobe, complementary to a target specific sequence to be detected in thesample. While microarrays may offer high multiplexing capability, theyare semi-quantitative and are inferior in terms of limit-of-detection(LOD) and detection dynamic range (DDR), due to their end-pointdetection nature (i.e., no real-time detection) and the fact that theylack any target amplification.

The present disclosure provides methods, devices and systems by whichone can achieve the multiplexing capabilities of microarrays whilehaving the LOD and DDR of Q-PCR methods. The methods and systemsprovided herein may be used to create unique nucleic acid detectionplatform and may find useful in a wide context of applications, such asmolecular diagnostics, DNA forensics, and pathogen genotyping, etc.

The methods, devices and systems described herein may be used forsimultaneously performing a plurality of reactions (e.g., a biochemicalreaction, a chemical reaction) and real-time monitoring the progress ofthe reactions via, for example, detecting and/or determining thepresence or absence, amount, quantity, concentration, activity and/orbinding characteristics of one or more target substances (e.g.,analytes, reagents and/or products including primers, amplicons, nucleicacid sequences) in a single reaction chamber. The amount, quantity,concentration, activity and/or binding characteristics of targetsubstances may be monitored and/or determined by detecting signalsproduced upon the occurrence of binding between the target substancesand the probes contained within multiple independently addressablelocations. With provided methods and systems of the present disclosure,the presence or absence of the target substances may be determined withhigh sensitivity and/or specificity. For example, the presence orabsence of a target analyte may be determined or detected at asensitivity of at least about 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, 99.999%, or 99.9999%.Similarly, the sensitivity of the methods provided herein may be atleast about 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, 99.9%, 99.99%, 99.999%, or 99.9999%.

The systems and methods provided herein may comprise a chip whichfurther comprises an integrated sensor array. The sensor array maycomprise a substrate and a plurality of probes (e.g., an array ofprobes) that attached or immobilized to a surface of the substrate. Thesensor array may also comprise a single or a plurality of integratedsensors that may be capable of detecting or capturing a signal producedonce the probes bind to one or more analytes (e.g., a target nucleicacid molecule, a template nucleic acid molecule, a primer, an amplicon,a polymerase) in a reaction mixture. As provided herein, any number ofsensors may be used. In some cases, a small number of sensors may beincluded. In some cases, a large number of sensors may be used. In somecases, a system may comprise less than or equal to about 1,000,000,750,000, 500,000, 250,000, 100,000, 75,000, 50,000, 25,000, 10,000,7,500, 5,000, 2,500, 1,000, 900, 800, 700, 600, 500, 400, 300, 200, 100,80, 60, 40, 20, 5, or 1 sensor. In some cases, a system may comprise atleast about 1, 10, 30, 50, 70, 90, 100, 300, 500, 700, 900, 1,100,1,500, 2,000, 4,000, 6,000, 8,000, 10,000, 20,000, 30,000, 40,000,50,000, 60,000, 70,000, 80,000, 90,000, 100,000, 250,000, or 500,000sensors. The sensors may be integrated sensors. The sensors can beindividually (or independently) addressable. In some cases, the numberof sensors comprised in a system may be between any of the two valuesdescribed herein, for example, about 12,500.

FIG. 1 shows an example multiplexed amplification and detection systemof the present disclosure. As FIG. 1 illustrates, the system comprises areaction chamber having a number of reagents (e.g., primer, templatenucleic acid molecule) required for a nucleic acid amplificationreaction, a probe array having three independently addressable locations(i.e., pixel [i], [i+1] and [i+2]) and a detector capable of real-timedetecting signals produced in each pixels. The probes are attached tothe substrate of the probe array via a linker. For each addressablelocation, a different type of probe that can specifically bind to asingle type of target substance (i.e., amplicons [i], [i+1] and [i+2]produced within each location) is included. Upon binding of the ampliconto the probe, signals reflective of the binding events on each pixel(i.e., signal [i], [i+1] and [i+2]) may be generated and captured by thedetector. By analyzing the detected signals, progress of amplificationreactions within each location may be determined in parallel.

The methods, devices and systems provided herein may utilize real-timemicroarray systems. Examples of such systems may be found in, forexample, U.S. Patent Pub. Nos. 2010/0122904, 2013/0345065, 2014/0001341,2014/0318958, 2014/0011710, 2012/0168306, 2013/0225441, 2012/0077692,2007/0099198, 2008/0081769, 2008/0176757 and 2008/0039339, and U.S. Pat.Nos. 8,637,436, 8,048,626, and 8,518,329, each of which is entirelyincorporated herein by reference.

Systems of the present disclosure may include at least one reactionchamber, a probe array and a detection system. The reaction chamber maybe configured to perform functions of one or more reactions (e.g.,nucleic acid amplification processes or PCR). The nucleic acidamplification processes may include biochemical processes that canspecifically increase the copy number of specific nucleotide sequencesand label the generated products (i.e., amplicons) with reportermolecules (i.e., “labels”) in a single reaction chamber. The reactionchamber can include an aqueous environment in which a plurality offree-moving analytes (e.g., nucleic acid sequences to be detected) orreagents (e.g., primers, probes, chemical surface modifiers andpolymerase) is present. The probe array may comprise a plurality ofnucleic acid probes at independently addressable locations on a solidsurface. Each addressable location (e.g., “pixel”) may include aplurality of identical nucleic acid sequences (or “probes”) that canspecifically hybridize or bind to a specific amplicon and/or othernucleic sequences in the reaction chamber. The probes and/or theanalytes may be labeled with one or more reporter molecules (e.g.,energy acceptors, energy donors). In some examples, the probes can belabeled with energy acceptors. The energy acceptors can be quenchers. Insuch a case, the analytes (such as dNTPs, primers) can be labeled withenergy donors. The energy donors can be fluorphores. As an alternative,the probes can be labeled with energy donors. The energy donors can befluorophores. In such a case, the analytes can be labeled with energyacceptors. The energy acceptors can be quenchers.

The detection system may comprise one or more detectors. The detectorcan real-time measure the generated signal in parallel at eachaddressable location that is indicative of the progress of the reaction.For example, for PCR reaction, the detected signal may be reflective ofthe presence and activity of reporter molecules in its vicinity, as thereaction progresses and the probe/target sequence interactions occur.

Reaction Chamber

The methods, devices and systems of the present disclosure may comprisea single reaction chamber or a plurality of reaction chambers. Thereaction chamber may comprise a plurality of sub-reaction chambers thatare in fluid communication with each other. The reaction chamber may beseparated from the probe array and detection system. The reactionchamber may be integrated with the probe array and/or the detectionsystem. The reaction chamber may comprise at least one sample inlet. Thereaction chamber may further in electric communication with atemperature control module is configured to alter, control and/ormaintain the temperature in the reaction chamber. The reaction chambermay be configured to retain a reaction mixture and facilitate anamplification reaction of one or more target analytes in the reactionmixture. The reaction mixture may comprise analytes such as, templatenucleic acid molecule to be amplified, primer pairs, limiting primers,excess primers, polymerases, nucleotides, solvent, or any other reagentsthat may be required for a reaction. Any of the analytes in the reactionmixture may be labeled by one or more reporter molecules. Binding of theprobes and analytes that comprise the reporter molecules may produce asignal that can be captured or detected by an integrated sensor. Suchsignal may be indicative of a presence or absence of one or moreanalytes in the reaction mixture, or the process of the reaction. Thesignals may be detected at a single time point or multiple time points.The signals may also be monitored in real-time. While detecting thesignals from the reaction mixture, the reaction mixture may or may notbe in contact with the sensor. In some cases, detecting signalscomprises measuring or determining an increase of a signal relative tobackground. In some cases, detecting signals comprises measuring orobserving a decrease of a signal relative to background. Backgroundsignal may refer to a signal detected or obtained prior the occurrenceof the binding event. The detecting may also comprise measuring ordetecting at least one control signal. The control signal may begenerated upon binding of the probes with a control sample having aknown sequence.

A reaction chamber can comprise a closed reservoir. The reaction chambercan have a volume from about 100 mL to about 1 nL. In some cases, thereaction chamber volume is from about 100 μL to about 1 μL.

A reaction chamber can contain a solution (e.g., an aqueous solution).The aqueous solution within the reaction chamber can comprise a bufferedsaline-based solution, such as an aqueous solution comprising a mixtureof a weak acid and its conjugate base, or vice versa. The solution cancomprise a plurality of target substances (e.g., nucleic acidsequences). The term “nucleic acid sequence” or “nucleotide sequence” asused in this context refers to nucleic acid molecules with a givensequence of nucleotides, of which it is desired to know the presenceand/or amount. The nucleotide sequence can comprise RNA or DNA, or asequence derived from RNA or DNA. Examples of nucleotide sequences aresequences corresponding to natural or synthetic RNA or DNA includinggenomic DNA and messenger RNA. The length of the sequence can be anylength that can be amplified into amplicons, for example up to about 5,10, 20, 50, 100, 200, 300, 400, 500, 600, 700, 800, 1,000, 1,200, 1,500,2,000, 5,000, 10,000 or more than 10,000 nucleotides in length.

In some cases, target analytes may include reporter molecules (e.g.,labels). The reporter molecules can comprise molecular structures that,once attached to a nucleic acid sequence, provide a distinctcharacteristic that is not inherent to those nucleic acid molecules.Examples are labels that create unique optical characteristics.

Probe Arrays

As described herein, the terms “array” and “microarray” can be usedinterchangeably. A probe array may comprise a surface having a pluralityof probes attached thereto, where the array can be used for thereal-time measurement and/or detection of the presence, amount,concentration, and/or binding characteristics of multiple analytes(e.g., amplicons). In some cases, one or more probes may be located on aplurality of discrete, isolated and independently addressable locations.

The substrate may be solid or semi-solid. The substrate may bebiological, non-biological, organic, inorganic, or a combination of anyof these, existing as a form of particles, strands, precipitates, gels,sheets, tubing, spheres, containers, capillaries, pads, slices, films,plates, slides, semiconductor integrated chips, etc. The substrate maytake on any surface configurations (e.g., flat). For example, thesubstrate may contain raised or depressed regions on which synthesis ordeposition may take place. In some cases, the substrate may be chosen toprovide appropriate light-absorbing characteristics. For example, thesubstrate may be a polymerized Langmuir Blodgett film, functionalizedglass, Si, Ge, GaAs, Gap, SiO₂, SiN₄, modified silicon, or any one of avariety of gels or polymers such as (poly)tetrafluoroethylene,(poly)vinylidenedifluoride, polystyrene, polycarbonate, or combinationsthereof.

The substrate may be a homogeneous solid and/or unmoving mass withdimensions much larger than the probes. In some cases, the probes may beconfined and/or immobilized within a certain distance of the substrate.The mass of the substrate may be at least 100 times larger than that ofthe probe. The surface of the substrate may be planar or non-planar.Examples of non-planar substrates may include spherical magnetic beads,spherical glass beads, and solid metal and/or semiconductor and/ordielectric particles. In cases where the substrate comprises a planarsurface, the roughness of the surface may vary. In some cases, theroughness of the substrate surface may be less than or equal to about1000 nanometers (nm), 750 nm, 500 nm, 250 nm, 100 nm, 90 nm, 80 nm, 70nm, 60 nm, 50 nm, 40 nm, 30 nm, 20 nm, 10 nm, 5 nm, 1 nm, 0.75 nm, 0.5nm, 0.25 nm, 0.1 nm, 0.05 nm, 0.25 nm, 0.01 nm, 0.005 nm, or 0.001 nm.In some cases, the surface of the substrate may have a roughness greaterthan or equal to about 0.0001 nm, 0.0005 nm, 0.001 nm, 0.005 nm, 0.01nm, 0.05 nm, 0.1 nm, 0.5 nm, 1 nm, 5 nm, 10 nm, 20 nm, 30 nm, 40 nm, 50nm, 60 nm, 70 nm, 80 nm, 90 nm, 100 nm, 200 nm, 300 nm, 400 nm, or 500nm. In some cases, the roughness of the substrate surface may be betweennay of the two values described herein, for example, about 75 nm.

The substrate can be optically clear, allowing transmission of the lightthrough the substrate, and excitation and/or detection to occur as thelight passing through the substrate. The substrate can also betranslucent or opaque. In some cases, the substrate can be reflective,allowing for light to pass through the surface layer containing probesand reflect back to a detector.

In some cases, the array may be incorporated into the reaction chamberin which the amplification reaction takes place. The array may be partof the wall or base of the chamber. The array may mate with othercomponents, forming a seal, and creating a reaction chamber for carryingout the amplification reaction.

The substrate can be made of various materials. Non-limiting examples ofmaterials may include silica, silicon, plastic, glass, metal,metal-alloy, nanopore, polymer, and nylon. Surface of the substrate canbe treated with a layer of chemicals prior to attaching probes toenhance the binding and/or to inhibit non-specific binding during use.For example, the substrate may comprise glass slide, which can be coatedwith self-assembled monolayer (SAM) coatings, such as coatings of asaminoalkyl silanes, or of polymeric materials, such as acrylamide andproteins. A variety of can be used, for example, 3D-Link® (Surmodics),EZ-Rays® (Mosaic Technologies), Fastslides® (Schleicher and Schuell),Superaldehyde®, and Superamine® (CEL Technologies).

Probes may be associated with, attached to, or bonded to the substrate.The association, attachment or bonding of the probes may be reversibleor irreversible. The association, attachment or bonding of the probesmay be chemical, biological, or biochemical. In some cases, the probesmay be associated with, attached to or bonded with the substrate via alinker. The linker may be any type of molecules (chemical or biological)that is capable of linking the probes with the substrate. In some cases,the linker can be a chemical bond. For example, the probes can beattached covalently to the surface of the substrate.

A number of different chemical surface modifiers can be added tosubstrates to attach the probes to the substrates. Examples of chemicalsurface modifiers may include, but not limited to, N-hydroxy succinimide(NHS) groups, amines, aldehydes, epoxides, carboxyl groups, hydroxylgroups, hydrazides, hydrophobic groups, membranes, maleimides, biotin,streptavidin, thiol groups, nickel chelates, photoreactive groups, borongroups, thioesters, cysteines, disulfide groups, alkyl and acyl halidegroups, glutathiones, maltoses, azides, phosphates, phosphines, andcombinations thereof. In one cases, substrate surfaces reactive towardsamines may be utilized. Examples of such surfaces may includeNHS-esters, aldehyde, epoxide, acyl halide, and thio-ester. Molecules(e.g., proteins, peptides, glycopeptides) with free amine groups mayreact with such surfaces to form covalent bond with the surfaces.Nucleic acid probes with internal or terminal amine groups can also besynthesized, (e.g., from IDT or Operon) and bound (e.g., covalently ornon-covalently) to surfaces using similar chemistries.

Surface of the substrate may or may not be reactive towards amines. Incases where an amine-reactive substrate is needed, the substrate surfacemay be converted into amine-reactive substrates with coatings.Non-limiting examples of coatings may include amine coatings (which canbe reacted with bis-NHS cross-linkers and other reagents), thiolcoatings (which can be reacted with maleimide-NHS cross-linkers, etc.),gold coatings (which can be reacted with NHS-thiol cross linkers, etc.),streptavidin coatings (which can be reacted with bis-NHS cross-linkers,maleimide-NHS cross-linkers, biotin-NHS cross-linkers, etc.), BSAcoatings (which can be reacted with bis-NHS cross-linkers, maleimide-NHScross-linkers, etc.), or combinations thereof. Alternatively, in somecases, the probes, rather than the substrate, can be reacted withspecific chemical modifiers to make them reactive to the respectivesurfaces.

A number of multi-functional cross-linking agents can be used to convertthe chemical reactivity of one type of surface to another. The agentscan be homo-functional or hetero-functional. The agents can bebi-functional, tri-functional, or tetra-functional, for example, abi-functional cross-linking agent X—Y—Z, with X and Z being two reactivegroups, and Y being a connecting linker. Further, if X and Z are thesame group, such as NHS-esters, the resulting cross-linker, NHS—Y—NHS,is a homo-bi-functional cross-linker and may connect an amine surfacewith an amine-group containing molecule. If X is NHS-ester and Z is amaleimide group, the resulting cross-linker, NHS-Y-maleimide, is ahetero-bi-functional cross-linker and may link an amine surface (or athiol surface) with a thio-group (or amino-group) containing probe.Examples of such agents may include, but not limited to NHS-esters,thio-esters, alkyl halides, acyl halides (e.g., iodoacetamide), thiols,amines, cysteines, histidines, di-sulfides, maleimide, cis-diols,boronic acid, hydroxamic acid, azides, hydrazines, phosphines,photoreactive groups (e.g., anthraquinone, benzophenone), acrylamide(e.g., acrydite), affinity groups (e.g., biotin, streptavidin, maltose,maltose binding protein, glutathione, glutathione-S-transferase),aldehydes, ketones, carboxylic acids, phosphates, hydrophobic groups(e.g., phenyl, cholesterol), and combinations thereof. Suchcross-linkers can be reacted with the surface or with the probes or withboth, in order to conjugate a probe to a surface.

Additionally or alternatively, a substrate may include thiol reactivesurfaces such as acrylate, maleimide, acyl halide and thio-estersurfaces. Such surfaces can covalently link proteins, peptides,glycopeptides, etc., via a thiol group. Nucleic acid probes containingpendant thiol-groups can also be easily synthesized.

Various alternative surface modification techniques may be utilized inthe present disclosure, for example, photo-crosslinkable surfaces andthermally cross-linkable surfaces. Examples of such techniques mayinclude Mosiac Technologies (Waltham, Mass.), Exigon™ (Vedbaek,Denmark), Schleicher and Schuell (Keene, N.H.), Surmodics™ (St. Paul,Minn.), Xenopore™ (Hawthorne, N.J.), Pamgene (Netherlands), Eppendorf(Germany), Prolinx (Bothell, Wash.), Spectral Genomics (Houston, Tex.),and Combimatrix™ (Bothell, Wash.).

Various materials may be used to fabricate the surface of the substrate.Exemplary materials may include glass, metal (e.g., gold, silicon,copper, titanium, and aluminum), metal oxides (e.g., titanium oxide,iron oxide), silicon-based material (e.g., silicon, silica), plastics,polymer (e.g., polystyrene, polyethylene, polypropylene), zeolites, andcombinations thereof. In some cases, the devices and systems providedherein may comprise LED (Light Emitting Diode) and OLED (Organic LightEmitting Diode) surfaces. An array of LEDs or OLEDs can be used at thebase of a probe array. Such systems may be advantageous since theyprovide easy optoelectronic methods of result readout. In some cases,the results can be read-out using a naked eye.

Probes can be deposited onto the substrates, e.g., onto a modifiedsurface, using either contact-mode printing methods using solid pins,quill-pins, ink-jet systems, ring-and-pin systems, etc. (see, e.g., U.S.Pat. Nos. 6,083,763 and 6,110,426) or non-contact printing methods(using piezoelectric, bubble-jet, syringe, electro-kinetic, mechanical,or acoustic methods. Example devices that may be used to deposit anddistribute probes onto substrate surfaces may include, e.g., devicesproduced by Packard Instruments or devices for depositing, e.g.,spotting, probes onto substrates include solid pins or quill pins(Telechem/Biorobotics).

As described elsewhere herein, the plurality of probes may be located onmultiple independently addressable locations (or regions) on thesubstrate. The addressable locations may be distributed evenly orunevenly across the substrate. In some cases, each of the addressablelocations may contain at least one probe. In some cases, only a certainpercentage of the addressable locations may contain probes. Theaddressable locations without probes may act as control spots in orderto increase the quality of the measurement, for example, by usingbinding to the spot to estimate and correct for non-specific binding. Insome cases, less than or equal to about 1, 5, 10, 20, 30, 40, 50, 60,70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000, 2,000,3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 25,000, 50,000,75,000, 100,000, 250,000, 500,000, 750,000, or 1,000,000 addressableregions may contain probes. In some cases, greater than or equal toabout 1, 10, 25, 50, 75, 100, 200, 400, 600, 800, 1,000, 2,000, 3,000,4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 25,000, 50,000,75,000, 100,000, 250,000, 500,000, 750,000, or 1,000,000 addressableregions may contain probes. In some cases, the number of addressablelocations that contain probes may be between any of the two valuesdescribed herein, for example, about 30,000.

Number of probes comprised in each occupied addressable location (i.e.,addressable location having at least one probe) may vary. In some cases,each occupied addressable location may contain the same number ofprobes. In some cases, each occupied addressable location may contain adifferent number of probes. In some cases, a certain percentage of theoccupied addressable locations may comprise the same or a differentnumber of probes, for example, about 5%, 10%, 20%, 30%, 40%, 50%, 60%,70%, 80%, 90%, or 100% of the occupied addressable locations may containthe same or a different number of probes.

In cases where more than one type of probes is utilized, probe typecontained in the occupied addressable locations may vary. In some cases,it may be preferred to have different types of probes contained in eachof the occupied addressable locations. In some cases, it may benecessary to have a certain percentage of the occupied addressablelocations that contain the same or a different type of probes, forexample, about 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or100% of the occupied addressable locations may contain the same or adifferent type of probes.

In some cases, it may be useful to have redundant addressable locationswhich have identical probes to another addressable location. Probearrays with such addressable location combinations can be lesssusceptible to fabrication non-idealities and measurement errors.

The shape of the cross-section of each addressable location may vary,for example, square, round, oval, triangle, rectangle, polygonal or anyother arbitrary shape.

The cross-sectional dimension of the addressable locations may vary. Insome cases, the addressable locations may have a large cross-sectionaldimension. In some cases, addressable locations with smallcross-sectional dimension may be used. In some cases, each side of thecross-section of the addressable location may be less than or equal toabout 1 millimeter (mm), 750 micron (μm), 500 μm, 250 μm, 100 μm, 50 μm,25 μm, 10 μm, 1 μm, 750 nm, 500 nm, 250 nm, 100 nm, 75 nm, 50 nm, 25 nm,10 nm, 5 nm, 1 nm, 0.5 nm, 0.1 nm, 0.05 nm, or 0.01 nm. In some cases,each side of the cross-section of the addressable location may begreater than or equal to about 0.001 nm, 0.005 nm, 0.0075 nm, 0.1 nm,0.5 nm, 0.75 nm, 1 nm, 25 nm, 50 nm, 75 nm, 100 nm, 250 nm, 500 nm, 750nm, 1 micron (μm), 10 μm, 20 μm, 50 μm, 75 μm, 100 μm, 250 μm, 500 μm,750 μm, or 1 mm. In some cases, each side of the addressable locationmay have a dimension falling between any of the values described herein,for example, about 5 μm. As will be appreciated, each addressablelocation may or may not have the same cross-sectional dimension.

The probes in the present disclosure may or may not be labeled with areporter molecule. The reporter molecule can be bound to the probe byvarious methods, such as hybridization. In some cases, specific labelscan be attached to the probes within the addressable locations, inaddition to the labels that are incorporated. In such systems, capturedtargets can result in two labels coming into intimate proximity witheach other in the location. This interaction between labels can createunique detectable signals. For example, when the labels on the targetand probe, respectively, are fluorescent donor and acceptor moietiesthat can participate in a fluorescent resonance energy transfer (FRET)phenomenon, FRET signals can be detected. However, in some cases theinteraction is not FRET.

In some cases, the analyte (e.g., dNTPs) in the reaction mixture islabeled with a first type of reporter molecule and the surface of anarray is labeled with a second type of report molecule, wherein thesecond type of report molecule is not linked to or associated with theprobe (e.g., a surface bound reporter molecule). Binding of the analyteto the probe will bring two types of reporter molecules into closeproximity and therefore results in a change of the signals (e.g., anincrease or a decrease) detected from the surface of the array or thereaction mixture. Such signal change may then be used to, e.g.,determine a presence or absence of the analyte. For example, the analyteand the array surface may be labeled with a quencher and alight-emitting reporter molecule (e.g., a fluorophore), respectively,and the fluorescence from the fluorophore on the surface is quenched (orreduced) upon binding of the analyte to the probe. While the quencherdoes not emit a light signal, there is no signal from the reactionmixture (or solution) interfering with the signal from the array, whichthen substantially diminishes the noise at the array surface and enablesthe real-time measurement of signals at the array surface.Alternatively, in some examples, quenching moieties (e.g., quenchers)are attached to the array surface and the analyte is tagged with alight-emitting reporter (e.g., a fluorescent label). Upon binding of theanalyte to the surface-bound probe, a decrease of fluorescent signalsfrom the reaction mixture can be detected.

Detection System

Also provided herein is a detection system having at least one detectorthat is configured to capture, detect and/or monitor signals from thearray. Various signals may be produced, such as optical, electrical,electrochemical, magnetic, mechanical, acoustic, or electromagneticsignals. The signals may be correlated with the presence, amount,concentration, and/or binding characteristics of one or more species(e.g., primers, amplicons, nucleic acid sequences, reporter molecules,polymerases, dNTPs, or any other analytes and reagents). The signals canbe reflective or indicative of the progress of one or more reactions(e.g., PCR amplification). The signals can be detected at a single timepoint or multiple time points, or in real-time.

The detection system may comprise a single detector or a plurality ofdetectors (e.g., an array of detector). The detector(s) may be fixed ormovable. The detectors may scan the probe array such that a givendetector detects signals from different addressable locations of thearray during the reaction process. In cases where a plurality ofdetectors is comprised in the detection system, the number of detectorsmay correspond to the same independently addressable locations containedin a probe array. For example, a fixed detector array may be used,wherein each of the detectors may correspond to an individualaddressable location of a probe array. Any number of detectors may beutilized in the detection system as provided herein, for example, about1, 10, 50, 100, 250, 500, 1,000, 2,500, 5,000, 7,500, 10,000, 25,000,50,000, 75,000, 100,000, 250,000, 500,000, 750,000, or 1,000,000detectors. The detectors may be comprised in the integrated sensors ofthe sensor array. Depending upon the type of singles to be detected,various types of detectors may be used, for example, optical detectors,electrical detectors, electrochemical detectors, or electrostaticdetectors. Examples of optical detectors may include but not limited tocharge-coupled device (CCDs) arrays (including cooled CCDs),complementary metal-oxide-semiconductor (CMOS) imagers, n-typemetal-oxide semiconductor (NMOS), active-pixel sensors (APS), orphotomultiplier tubes (PMTs). The detectors can also includewavelength-selective components such as optical filters to allowmeasurement of selective wavelengths. Examples of other detectors mayinclude electrodes.

The detector can sample (e.g., acquire measurements) at a rate of atleast about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 56, 57, 58, 59, 60, 90, 120, 150, 180, 210, 240, 270, 300, 400,500, 1000, 10,000, or 100,000 times per minute. The detector can sampleat a rate of at least about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9,1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3,2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7,3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 6, 7,8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85,90, 95, 100, 105, 110, 115, or 120 Hz.

The detection system can comprise a light source. The light source cancomprise at least one lamp, such as an incandescent, halogen,fluorescent, gas-discharge, arc, or light emitting diode (LED). Thelight source can comprise a laser. The light source can produce aspecific wavelength or range or wavelengths, such as UV. The lightsource can comprise filters for controlling the output wavelength orwavelengths. The light source can comprise multiple light sources, ofthe same or of different types, which can be used separately or incombination.

The detector can comprise various optical elements, including but notlimited to filters, lenses, collimators, mirrors, reflectors, beamsplitters, and diffusers. The detector can comprise a filter or aplurality of filters, including but not limited to wavelength filters(e.g., color filters, UV filters, IR filters), dichroic filters, andpolarizing filters. The filters can comprise multiple filters, of thesame or of different types, which can be used separately or incombination. The detector can comprise elements (e.g., signal processingunit) for removing image distortion or aberration, such as barrel orfisheye distortion, pincushion distortion, mustache distortion,monochromatic aberrations (e.g., piston, tilt, defocus, sphericalaberration, coma, astigmatism, field curvature, image distortion), orchromatic aberrations (e.g., axial, longitudinal, lateral, transverse).Such elements can comprise computer systems programmed to implementinstructions for partially or fully correcting image distortion. Forexample, Brown's distortion model or the Brown-Conrady model can be usedto correct for radial distortion and tangential distortion. In someexamples, the detector can measure emitted photons coming fromindividual addressable locations. These photons can be correlated to thepresence and/or activity of reporter molecules in that location.

As discussed elsewhere herein, parallel detection of nucleic acid (e.g.,DNA) hybridization reactions as a function of temperature in real timecan be performed by interaction between an immobilized probe labeledwith an energy donor (e.g., a fluorophore) at a specific pixels and atarget labeled with an energy acceptor (e.g., a quencher) that ispresent in the reaction chamber. Detection can also be performed byinteraction between an intercalator and interacting probes and targetsin a similar setting. The temperature of the reaction chamber can bevaried, while an optical detector continually measures the signal inreal time, to capture the amount of hybridized targets at individualpixels and evaluate whether the hybridization reaction is favorable ornot in that given temperature at that pixel.

In some cases, signals that signify hybridization reactions are onlygenerated at, and are confined to the pixels of the addressable arraywhile the reaction volume which includes all the targets creates minimumbackground optical signal. This unique characteristic not only improvethe detectable signal-to-interference (or signal-to-noise), but alsoenables multiplexing capabilities as the pixel-level measurementsremains independent of one another. This is despite the fact that thereaction chamber and aqueous sample is shared among all of them.

FIGS. 2-4 illustrate exemplary optical detection methods of the presentdisclosure. As shown in FIG. 2, primers to be used for the followingamplification reaction may be labeled with reporter molecules (e.g.,energy acceptors, donors, and/or quenchers). As the amplificationreaction proceeds, the reporter molecules may be incorporated into theamplified products (i.e., amplicons). Progress of the amplificationreaction may be monitored in real-time by detecting the change ofsignals upon the hybridization/binding of the amplicons or primers tothe probes. In example method A, prior to binding, the donor on theprobe is actively radiating signal. Once the probe binds to the target(i.e., quencher-labeled amplicon), the quencher bound to the targetquenches the signal from the energy donor bound to the probe, whichresults in a decrease or disappearance of the signal. In example methodB, energy donor-labeled probe keeps emitting/radiating signals untilbinding between the acceptor-incorporated amplicon and the probe occurs.A hairpin structure may be formed in the amplicon to facilitate thebinding between the amplicon and the probe. Once thehybridization/binging is completed, a reduction in energy donor signalmay be detected, indicating the ongoing of the amplification reaction.In method C, instead of binding to the amplified products, the probe isdesigned and configured to bind to the primers. The binding between theprimer and the probe may result in a reduction of signal produced by thedonor-labeled probe prior to the binding. As the amplification reactionproceeds, more primers may be consumed. Such decrease in the amount ofprimers free in the solution may be detected and hence indicative of theprogress of the reaction.

As discussed elsewhere herein, in some cases, the detection of targetsubstances may be realized via the use of other molecules, for example,an intercalator. Under such circumstances, no labeling for primer oramplicon is required, which greatly diminishes the background noisesproduced from the reaction solution. As shown in FIG. 3, in method A,the intercalator is inactive and produces little to no signal in theabsence of the binding. Once the hybridization/binding occurs betweenthe unlabeled amplicon and the probe, the intercalator becomes activatedand radiates a signal. In method B, the probe may be labeled by adeactivated energy acceptor which without binding to target substancesproduces little to no signal. The binding between the probe and theamplicon may then bring the intercalator and the deactivated acceptorinto close proximity. The energy transfer between the intercalator andthe acceptor may result in an increase of the signal. In method C, aprobe is labeled with a donor and there may be deactivated acceptorsfreely-moving in the solution. Prior to the binding of an amplicon tothe probe, the donor on the probe may be actively radiating signal dueto the large distance between the donor and acceptor. The binding of theamplicon to the probe may bring the acceptors in close proximity to theenergy donor on the probe, resulting in a decrease or disappearance ofthe signal.

FIG. 4 shows an example optical detection method by using labeled dNTP.As FIG. 4 shows, one or more dNTPs may be labeled with a reportermolecule, for example, an acceptor. As the amplification reactionproceeds and the template nucleic acid sequence gets replicated andelongated, the labeled dNTPs become incorporated into the amplifiedproducts (i.e., amplicons). The amplicons may be able to bind to theprobe which is labeled with a different type of reporter molecule, e.g.,a donor. In cases where the probe is donor-labeled, it may produce oremit signals without binding to any other substances. The producedsignals may be reduced or diminished once the amplicon binds to theprobe.

FIGS. 5-7 show exemplary electrical detection methods of the presentdisclosure. In such methods, target substances (e.g., primers,amplicons, dNTPs) and/or probes may be labeled by one or more reportermolecules (e.g., redox species) that are capable of producing orgenerating electrical signals to be detected by the detection system. Insome cases, neither the target substances nor the probes are labeledwith the reporter molecules and the signal may be generated with the useof other molecules, for example, an intercalator. For methods andsystems that utilize electrical detection methods, one or moreelectrodes may be used to acquire the signals. The electrodes may beseparated from or associated with the probe array. The electrodes may beintegrated with the probe array and/or the detection system. Theelectrodes may be further integrated with a computer control system thatis configured to implement the methods provided herein. In some cases,the electrodes may be embedded in the substrate of the probe array andcorrespond to each of the addressable locations (e.g., pixels) of thearray. The signals produced from each of the locations may be real-timedetected and/or monitored in parallel.

FIG. 5 shows an example electrical detection method by using labeledprimers. As the figure shows, the primers may be labeled with redoxspecies which may then be incorporated into the amplified products oncethe amplification reaction starts. In method A, prior to the binding,the probe produces little to no signals. As the amplification reactionproceeds and the amplicon starts to bind to the probe, thehybridization/binding of the amplicon result in an increase of thesignal, which in turn indicates the progress of the amplificationreaction. In method B, a hairpin structure may be formed in amplicon tofacilitate the binding between the amplicon and the probe. Or, theformation of the hairpin loop may be required to bring the amplicon andthe probe into close proximity such that a detectable signal may beproduced once the binding occurs. By detecting the signal change and/orintensities, the progress and/or degree of the amplification reactioncan be determined. In method C, a labeled primer instead of an ampliconis captured or bound to the probe. The quantity or amount of the primersin the reaction mixture can be easily determined by monitoring thechange of signal intensities generated via the binding between primersand probes. A decrease in the quantity or amount of the primers may thenbe reflective of the progress of the amplification reaction.

For methods illustrated in FIG. 6, no labeling is required. As shown inthis figure, prior to the binding, an electrochemical intercalator isfree-flowing in the reaction mixture and produces little to nosignal(s), and little to no reporter molecules are comprised in probesand amplicons. Therefore, before the binding occurs, no signals can bedetected from the reaction mixture. As the amplification reactionproceeds and the amplicon begins to bind to the probe, the intercalatormay be activated and start to produce signals for detection.

As provided elsewhere herein, any substances in reaction mixture may belabeled with one or more reporter molecules. In method shown in FIG. 7,dNTPs may be labeled by reporter molecules (e.g., electrochemical redoxlabels). These labels may be incorporated into amplicons later on as theamplification reaction proceeds. As shown in FIG. 7, prior to thebinding, the probe produces little to no signals. Once thehybridization/binding occurs, signals may be produced and detected.

System of the present disclosure may comprise an integrated biosensorarray having a plurality of integrated biosensors. An example advantageof using integrated biosensors, rather than conventional detectionapparatuses, is the drastic reduction is size and lower cost.Furthermore, integrated biosensor arrays can be manufactured usingsemiconductor integrated circuit (IC) micro-fabrication processes, e.g.,complementary metal-oxide-semiconductor (CMOS), which can offerunmatched reliability, high-volume manufacturing, and reliability.Examples of sensors that may be used with integrated biosensors arraysof the present disclosure are provided in U.S. Patent Pub. Nos.2010/0122904, 2013/0345065, 2014/0001341, 2014/0318958, 2014/0011710,2012/0168306, 2013/0225441, 2012/0077692, 2007/0099198, 2008/0081769,2008/0176757 and 2008/0039339, and U.S. Pat. Nos. 8,637,436, 8,048,626,and 8,518,329, each of which is entirely incorporated herein byreference.

In such arrangements, each sensor element can be addressable and caninclude its own probe. Such sensor element may be a biosensor. The arraycan comprise a number of individual biosensors, such as at least about100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000,5000, 6000, 7000, 8000, 9000, 10000, 15000, 20000, 25000, 30000, 35000,40000, 45000, 50000, 55000, 60000, 65000, 70000, 75000, 80000, 85000,90000, 95000, or 100000 integrated biosensors. The density of individualbiosensor in the array can be at least about 100, 200, 300, 400, 500,1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000 biosensorpixels per mm².

A biosensor in the array can comprise a photo-sensor, such as aphotodiode. Each biosensor can also be associated with temperaturecontrol elements as well, such as heaters and temperature sensors (e.g.,thermocouples, thermistors). The biosensor array can comprise opticalfilters, such as emission filters, between the photo-sensors and thereaction chambers or array pixels as described in, for example, in U.S.Patent Pub. Nos. 2010/0122904, 2013/0345065, 2014/0001341, 2014/0318958,2014/0011710, 2012/0168306, 2013/0225441 and 2008/0081769, and U.S. Pat.Nos. 8,637,436 and 8,518,329, each of which is entirely incorporatedherein by reference.

FIG. 10 shows an optical CMOS biochip detector (FIG. 10, top left)comprising a 32 by 32 array of optical biosensors (FIG. 10, top right).Each optical biosensor is about 100 micrometers square (mm²). Each sideof the optical biosensor array is about 3.2 mm in length. Each biosensorcomprises a photodiode sensor, and an emission filter is located betweenthe CMOS substrate of the biosensor and the reaction chamber of theassociated array pixel (FIG. 10, bottom left). The heat of the array canbe controlled by heaters (FIG. 10, bottom right).

FIG. 11 shows example circuit architecture for an optical CMOS biochip.Each of the 1024 pixels comprises a reaction chamber associated with aphotodiode circuit, separated by an emission filter. Each pixel furthercomprises a heater, a digital controller, and signal input/output forcalibration and data collection. The biochip further comprises a digitalcontroller. The digital controller interfaces with a scan module capableof row/column selection of biochip pixels for receiving data. Thedigital controller also interfaces with a thermal controller capable ofcontrolling the on-chip temperature. A power management system (e.g., 5volts) provides power to the pixels and the thermal controller.

An electrical CMOS biochip detector is shown in FIG. 12. The examplebiochip detector (FIG. 12, top left) comprises a 32×32 array ofelectrical biosensors (FIG. 12, top right). Each electrical biosensor isabout 100 micrometers square (mm²). Each side of the biosensor array isabout 3.2 mm in length. Each biosensor comprises a probe array locatedbetween the CMOS substrate of the biosensor and the reaction chamber ofthe associated array pixel (FIG. 12, bottom left). Each of thebiosensors may comprise a reference electrode (R) underneath a workingelectrode (W), a counter electrode (C) disposed in between two heaterlayers. The heat of the array can be controlled by heaters (FIG. 12,bottom right).

Example circuit architecture for an electrical CMOS biochip is shown inFIG. 13. As the figure shows, each of the 1024 pixels comprises areaction chamber associated with an electrical detection circuit havinga working electrode, a reference electrode and a counter electrode. Eachpixel further comprises a heater, a digital controller, and signalinput/output for calibration and data collection. The biochip furthercomprises a digital controller. The digital controller interfaces with ascan module capable of row/column selection of biochip pixels forreceiving data. The digital controller also interfaces with a thermalcontroller capable of controlling the on-chip temperature. A powermanagement system (e.g., 5 volts) provides power to the pixels and thethermal controller.

Nucleic Acid Amplification

Methods, devices and systems provided herein can be used for performingnucleic acid amplification reaction on a plurality of nucleotidesequences in a fluid that is in contact with an array of probes disposedin a plurality of independently addressable locations. The presence,quantity and/or binding activity of the amplified products (i.e.,amplicons) within each probe-comprising addressable location may besimultaneously detected and monitored in real-time as the reactionproceeds. Methods of amplification may include, for example, polymerasechain reaction (PCR), strand displacement amplification (SDA), andnucleic acid sequence based amplification (NASBA), and Rolling CircleAmplification (RCA).

The amplification method can be temperature cycling or be isothermal.The amplification method can be exponential or linear. Foramplifications with temperature cycling, a temperature cycle maygenerally correspond to an amplification cycle. Isothermalamplifications can in some cases have amplification cycles, such asdenaturing cycles, and in other cases, the isothermal amplificationreaction will occur monotonically without any specific amplificationcycle.

The amplification method may be used to amplify specific regions (i.e.,target regions), or nucleotide sequences of a nucleic acid molecule(e.g., DNA, RNA). This region can be, for example, a single gene, a partof a gene, or a non-coding sequence.

The amplification method may comprise: (1) a template that contains theregion of the nucleic acid sequence to be amplified; (2) one or moreprimers, which are complementary to the target region at the 5′ and 3′ends of the region that is to be amplified; (3) a polymerase (e.g. Taqpolymerase), used to synthesize a copy of the region to be amplified;(4) deoxynucleotide triphosphates (dNTPs); (5) a buffer solution, whichprovides a suitable chemical environment for optimum activity andstability of the polymerase; and/or (6) a divalent cation such asmagnesium or manganese ions.

A primer may be a nucleic acid strand, or a related molecule that servesas a starting point for nucleic acid replication. A primer may often berequired because some nucleic acid polymerases cannot begin synthesizinga new strand from scratch, but can only add to an existing strand ofnucleotides. The length of the primers may vary. Primers with longer orshorter lengths may be used, dependent upon, the application. Forexample, in some cases, chemically synthesized DNA molecules with alength about 10 to about 30 bases may be used as primers. In some cases,the length of primers can be for example about 20-30 nucleotides, andthe sequence of the primers are complementary to the beginning and theend of the target fragment to be amplified. The primers may anneal(adhere) to the template at these starting and ending points, wherepolymerase binds and begins the synthesis of the new strand. In somecases, degenerate primers may be used. Degenerate primers comprisemixtures of similar, but not identical, primers.

In some cases, asymmetric (or non-symmetric) amplification processes(e.g., asymmetric PCR) may be utilized. A primer pair compressing alimiting primer and an excess primer may be used in an asymmetricamplification process. The limiting primer may be present at a muchlower concentration than the excess primer. The asymmetric amplificationprocesses may preferentially amplify one strand in a double-strandednucleic acid template by using an excess of a primer for the strandtargeted for amplification. As the amplification reaction progresses,the limiting primer may be used up.

As provided in the present disclosure, primers may or may not be labeledwith a reporter molecule (e.g., a label). The labeled primers may beconfigured to facilitate and/or enable the detection and/or monitoringof the presence, quantity, concentration or binding activity of theprimers, amplicons, or other analytes. The reporter molecule may beincorporated into the amplified products as the amplification reactionproceeds. The primers may be labeled with one or more reportermolecules. The reporter molecules can be optical, electrical orelectrochemical. Examples of reporter molecules may include, but notlimited to fluorescent, quenchers, fluorophores, members of afluorescence resonance energy transfer (FRET) pair, redox species, orcombinations thereof.

In cases where an asymmetric amplification process is utilized, eachprimer in a primer pair may be labeled with the same or a different typeof reporter molecules. As described elsewhere herein, the systems,devices and methods of the present disclosure may comprise an arrayhaving a plurality of independently addressable locations (e.g.,pixels). Each of the addressable locations may or may not contain one ormore probes that are configured to be able to capture one or morespecies in the reaction chamber (e.g., primers, amplicons, polymerases,dNTPs, or any other analytes and reagents). The probes may or may not belabeled by one or more reporter molecules. The labeled probes may or maynot be able to produce signals (e.g., optical, electrical,electrochemical, magnetic, mechanical, acoustic, or electromagneticsignals) that can be detected or monitored by a detection systemprovided in the present disclosure. The detected signal may beindicative or reflective of a progress of a reaction (e.g., a nucleicacid amplification progress). In some cases, each of the addressablelocations may comprise the same type of probes, for example, probes thatare capable to capture a specific target nucleic acid sequence. In somecases, it may be preferred to have an array in which each of theaddressable locations contains a different type of probes. Each type ofthe probes may be used to specifically capture and thereforedetect/monitor a certain type of target substances (e.g., a primer, anamplicon etc.) as the reaction progresses. In some cases, it may beuseful to have at least two different types of probes that are able tocapture and/or detect at least two different type of target substances.

Example amplification methods of the present disclosure, along withconcentration profiles of primers and amplicons in the methods are shownin FIG. 8. As FIG. 8 shows, in amplification reaction, a primer pair isused. Depending upon, whether there is a difference betweenconcentrations of the primers, an asymmetric PCR amplification or aconventional amplification method may be utilized. For example, if fortwo primers in a pair, [P(+)] is the same or substantially the same as[P(−)], then a convention amplification reaction is conducted. However,if the concentration of one primer is largely different from the otherone in the pair, for example, [P(+)] [P(−)], then an asymmetricalamplification method is used. As described elsewhere herein, thequantity, amount, and/or concentration of one or more target substancescontained in reaction mixture (e.g., primers, amplicons, dNTPs) may bedetected or monitored in real-time with the methods and systems of thepresent disclosure. By following or monitoring thequantity/concentration change of at least one substance, the progress ofthe amplification reaction may be determined (FIG. 8, bottom left andbottom right).

A wide variety of fluorescent molecules (e.g., small molecules,fluorescent proteins and quantum dots) can be utilized in the presentdisclosure. Non-limiting examples of fluorescent molecules (orfluorophores) may include: 1,5 IAEDANS; 1,8-ANS; 4-Methylumbelliferone;5-carboxy-2,7-dichlorofluorescein; 5-Carboxyfluorescein (5-FAM);5-Carboxynapthofluorescein; 5-Carboxytetramethylrhodamine (5-TAMRA);5-FAM (5-Carboxyfluorescein); 5-HAT (Hydroxy Tryptamine); 5-HydroxyTryptamine (HAT); 5-ROX (carboxy-X-rhodamine); 5-TAMRA(5-Carboxytetramethylrhodamine); 6-Carboxyrhodamine 6G; 6-CR 6G; 6-JOE;7-Amino-4-methylcoumarin; 7-Aminoactinomycin D (7-AAD);7-Hydroxy-4-methyl coumarin; 9-Amino-6-chloro-2-methoxyacridine; ABQ;Acid Fuchsin; ACMA (9-Amino-6-chloro-2-methoxyacridine); AcridineOrange; Acridine Red; Acridine Yellow; Acriflavin; Acriflavin FeulgenSITSA; Aequorin (Photoprotein); AFPs—AutoFluorescent Protein—(QuantumBiotechnologies); Alexa Fluor 350™; Alexa Fluor 430™; Alexa Fluor 488™;Alexa Fluor 532™; Alexa Fluor 546™; Alexa Fluor 568™; Alexa Fluor 594™;Alexa Fluor 633™; Alexa Fluor 647™; Alexa Fluor 660™; Alexa Fluor 680™;Alizarin Complexion; Alizarin Red; Allophycocyanin (APC); AMC, AMCA-S;AMCA (Aminomethylcoumarin); AMCA-X; Aminoactinomycin D; Aminocoumarin;Aminomethylcoumarin (AMCA); Anilin Blue; Anthrocyl stearate; APC(Allophycocyanin); APC-Cy7; APTRA-BTC; APTS; Astrazon Brilliant Red 4G;Astrazon Orange R; Astrazon Red 6B; Astrazon Yellow 7 GLL; Atabrine;ATTO-TAG™ CBQCA; ATTO-TAG™ FQ; Auramine; Aurophosphine G; Aurophosphine;BAO 9 (Bisaminophenyloxadiazole); BCECF (high pH); BCECF (low pH);Berberine Sulphate; Beta Lactamase; Bimane; Bisbenzamide; Bisbenzimide(Hoechst); bis-BTC; Blancophor FFG; Blancophor SV; BOBO™-1; BOBO™-3;Bodipy 492/515; Bodipy 493/503; Bodipy 500/510; Bodipy 505/515; Bodipy530/550; Bodipy 542/563; Bodipy 558/568; Bodipy 564/570; Bodipy 576/589;Bodipy 581/591; Bodipy 630/650-X; Bodipy 650/665-X; Bodipy 665/676;Bodipy FI; Bodipy FL ATP; Bodipy FI-Ceramide; Bodipy R6G SE; Bodipy TMR;Bodipy TMR-X conjugate; Bodipy TMR-X, SE; Bodipy TR; Bodipy TR ATP;Bodipy TR-X SE; BO-PRO™-1; BO-PRO™-3; Brilliant Sulphoflavin FF; BTC;BTC-SN; Calcein; Calcein Blue; Calcium Crimson™; Calcium Green; CalciumGreen-1 Ca.sup.2+Dye; Calcium Green-2 Ca.sup.2+; Calcium Green-SNCa.sup.2+; Calcium Green-C18 Ca.sup.2.sup.+; Calcium Orange; CalcofluorWhite; Carboxy-X-rhodamine (5-ROX); Cascade Blue™; Cascade Yellow;Catecholamine; CCF2 (GeneBlazer); CFDA; Chlorophyll; Chromomycin A;Chromomycin A; CL-NERF; CMFDA; Coumarin Phalloidin; C-phycocyanine; CPMMethylcoumarin; CTC; CTC Formazan; Cy2™; Cy3.1 8; Cy3.5™; Cy3™; Cy5.1 8;Cy5.5™; Cy5™; Cy7™; cyclic AMP Fluorosensor (FiCRhR); Dabcyl; Dansyl;Dansyl Amine; Dansyl Cadaverine; Dansyl Chloride; Dansyl DHPE; Dansylfluoride; DAPI; Dapoxyl; Dapoxyl 2; Dapoxyl 3′ DCFDA; DCFH(Dichlorodihydrofluorescein Diacetate); DDAO; DHR (Dihydrorhodamine123); Di-4-ANEPPS; Di-8-ANEPPS (non-ratio); DiA (4-Di-16-ASP);Dichlorodihydrofluorescein Diacetate (DCFH); DiD—Lipophilic Tracer; DiD(DiIC18(5)); DIDS; Dihydrorhodamine 123 (DHR); Dil (DiIC18(3));Dinitrophenol; DiO (DiOC18(3)); DiR; DiR (DiIC18(7)); DM-NERF (high pH);DNP; Dopamine; DTAF; DY-630-NHS; DY-635-NHS; ELF 97; Eosin; Erythrosin;Erythrosin ITC; Ethidium Bromide; Ethidium homodimer-1 (EthD-1);Euchrysin; EukoLight; Europium (III) chloride; EYFP; Fast Blue; FDA;Feulgen (Pararosaniline); FIF (Formaldehyde Induced Fluorescence); FITC;Flazo Orange; Fluo-3; Fluo-4; Fluorescein (FITC); Fluorescein Diacetate;Fluoro-Emerald; Fluoro-Gold (Hydroxystilbamidine); Fluor-Ruby; Fluor X;FM 1-43™; FM 4-46; Fura Red™ (high pH); Fura Red™/Fluo-3; Fura-2;Fura-2/BCECF; Genacryl Brilliant Red B; Genacryl Brilliant Yellow 10GF;Genacryl Pink 3G; Genacryl Yellow 5GF; GeneBlazer (CCF2); Gloxalic Acid;Granular blue; Haematoporphyrin; Hoechst 33258; Hoechst 33342; Hoechst34580; HPTS; Hydroxycoumarin; Hydroxystilbamidine (FluoroGold);Hydroxytryptamine; Indo-1, high calcium; Indo-1, low calcium;Indodicarbocyanine (DiD); Indotricarbocyanine (DiR); Intrawhite Cf;JC-1; JO-JO-1; JO-PRO-1; LaserPro; Laurodan; LDS 751 (DNA); LDS 751(RNA); Leucophor PAF; Leucophor SF; Leucophor WS; Lissamine Rhodamine;Lissamine Rhodamine B; Calcein/Ethidium homodimer; LOLO-1; LO-PRO-1;Lucifer Yellow; Lyso Tracker Blue; Lyso Tracker Blue-White; Lyso TrackerGreen; Lyso Tracker Red; Lyso Tracker Yellow; LysoSensor Blue;LysoSensor Green; LysoSensor Yellow/Blue; Mag Green; Magdala Red(Phloxin B); Mag-Fura Red; Mag-Fura-2; Mag-Fura-5; Mag-indo-1; MagnesiumGreen; Magnesium Orange; Malachite Green; Marina Blue; Maxilon BrilliantFlavin 10 GFF; Maxilon Brilliant Flavin 8 GFF; Merocyanin;Methoxycoumarin; Mitotracker Green FM; Mitotracker Orange; MitotrackerRed; Mitramycin; Monobromobimane; Monobromobimane (mBBr-GSH);Monochlorobimane; MPS (Methyl Green Pyronine Stilbene); NBD; NBD Amine;Nile Red; Nitrobenzoxadidole; Noradrenaline; Nuclear Fast Red; NuclearYellow; Nylosan Brilliant lavin EBG; Oregon Green; Oregon Green 488-X;Oregon Green™; Oregon Green™ 488; Oregon Green™ 500; Oregon Green™ 514;Pacific Blue; Pararosaniline (Feulgen); PBFI; PE-Cy5; PE-Cy7; PerCP;PerCP-Cy5.5; PE-TexasRed [Red 613]; Phloxin B (Magdala Red); PhorwiteAR; Phorwite BKL; Phorwite Rev; Phorwite RPA; Phosphine 3R; PhotoResist;Phycoerythrin B [PE]; Phycoerythrin R [PE]; PKH26 (Sigma); PKH67; PMIA;Pontochrome Blue Black; POPO-1; POPO-3; PO-PRO-1; PO-PRO-3; Primuline;Procion Yellow; Propidium lodid (PL); PyMPO; Pyrene; Pyronine; PyronineB; Pyrozal Brilliant Flavin 7GF; QSY 7; Quinacrine Mustard; Red 613[PE-TexasRed]; Resorufin; RH 414; Rhod-2; Rhodamine; Rhodamine 110;Rhodamine 123; Rhodamine 5 GLD; Rhodamine 6G; Rhodamine B; Rhodamine B200; Rhodamine B extra; Rhodamine BB; Rhodamine BG; Rhodamine Green;Rhodamine Phallicidine; Rhodamine Phalloidine; Rhodamine Red; RhodamineWT; Rose Bengal; R-phycocyanine; R-phycoerythrin (PE); S65A; S65C; S65L;S65T; SBFI; Serotonin; Sevron Brilliant Red 2B; Sevron Brilliant Red 4G;Sevron Brilliant Red B; Sevron Orange; Sevron Yellow L; SITS; SITS(Primuline); SITS (Stilbene Isothiosulphonic Acid); SNAFL calcein;SNAFL-1; SNAFL-2; SNARF calcein; SNARF1; Sodium Green; SpectrumAqua;SpectrumGreen; SpectrumOrange; Spectrum Red; SPQ(6-methoxy-N-(3-sulfopropyl)quinolinium); Stilbene; Sulphorhodamine Bcan C; Sulphorhodamine Extra; SYTO 11; SYTO 12; SYTO 13; SYTO 14; SYTO15; SYTO 16; SYTO 17; SYTO 18; SYTO 20; SYTO 21; SYTO 22; SYTO 23; SYTO24; SYTO 25; SYTO 40; SYTO 41; SYTO 42; SYTO 43; SYTO 44; SYTO 45; SYTO59; SYTO 60; SYTO 61; SYTO 62; SYTO 63; SYTO 64; SYTO 80; SYTO 81; SYTO82; SYTO 83; SYTO 84; SYTO 85; SYTOX Blue; SYTOX Green; SYTOX Orange;Tetracycline; Tetramethylrhodamine (TRITC); Texas Red™; Texas Red-X™conjugate; Thiadicarbocyanine (DiSC3); Thiazine Red R; Thiazole Orange;Thioflavin 5; Thioflavin S; Thioflavin TCN; Thiolyte; Thiozole Orange;Tinopol CBS (Calcofluor White); TMR; TO-PRO-1; TO-PRO-3; TO-PRO-5;TOTO-1; TOTO-3; TriColor (PE-Cy5); TRITCTetramethylRodaminelsoThioCyanate; True Blue; TruRed; Ultralite; UranineB; Uvitex SFC; WW 781; X-Rhodamine; XRITC; Xylene Orange; Y66F; Y66H;Y66 W; YO-PRO-1; YO-PRO-3; YOYO-1; YOYO-3, Sybr Green, Thiazole orange(interchelating dyes), Alexa Fluor dye series (e.g., Alexa Fluor 350,Alexa Fluor 405, 430, 488, 500, 514, 532, 546, 555, 568, 594, 610, 633,635, 647, 660, 680, 700, and 750), Cy Dye fluorophore series (e.g., Cy3,Cy3B, Cy3.5, Cy5, Cy5.5, Cy7), Oyster dye fluorophores (e.g.,Oyster-500, -550, -556, 645, 650, 656), DY-Labels series (e.g., DY-415,-495, -505, -547, -548, -549, -550, -554, -555, -556, -560, -590, -610,-615, -630, -631, -632, -633, -634, -635, -636, -647, -648, -649, -650,-651, -652, -675, -676, -677, -680, -681, -682, -700, -701, -730, -731,-732, -734, -750, -751, -752, -776, -780, -781, -782, -831, -480XL,-481XL, -485XL, -510XL, -520XL, -521XL), ATTO fluorescent labels (e.g.,ATTO 390, 425, 465, 488, 495, 520, 532, 550, 565, 590, 594, 610, 611X,620, 633, 635, 637, 647, 647N, 655, 680, 700, 725, 740), CAL Fluor andQuasar dyes (e.g., CAL Fluor Gold 540, CAL Fluor Orange 560, Quasar 570,CAL Fluor Red 590, CAL Fluor Red 610, CAL Fluor Red 635, Quasar 670),quantum dots (e.g., Qdot 525, Qdot565, Qdot585, Qdot605, Qdot655,Qdot705, Qdot 800), fluorescein, rhodamine, phycoerythrin, orcombinations thereof.

Molecules that can be used in FRET may include fluorophores as describedabove, fluorescein, 5-carboxyfluorescein (FAM),2′7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), rhodamine,6-carboxyrhodamine (R6G), N,N,N′,N′-tetramethyl-6-carboxyrhodamine(TAMRA), 6-carboxy-X-rhodamine (ROX), 4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL), and 5-(2′-aminoethyl)aminonaphthalene-1-sulfonicacid (EDANS).

In some cases, the acceptor of the FRET pair may be used to quench thefluorescence of the donor. The acceptor may have little to nofluorescence. In some cases, the FRET acceptors that are useful forquenching may be referred to as quenchers. Non-limiting examples ofquenchers may include, Black Hole Quencher Dyes (e.g., BHQ-0, BHQ-1,BHQ-2, BHQ-3, BHQ-10), QSY Dye fluorescent quenchers (e.g., QSY7, QSY9,QSY21, QSY35), Dabcyl and Dabsyl, Cy5Q, Cy7Q, Dark Cyanine dyes (whichcan be used, for example, in conjunction with donor fluors such as Cy3B,Cy3, or Cy5), DY-Quenchers (e.g., DYQ-660 and DYQ-661), ATTO fluorescentquenchers (e.g., ATTO 540Q, 580Q, 612Q), or combinations thereof.

Target Substance/Probe Binding

Methods, devices and systems provided herein may be utilized to measure,monitor and/or detect the hybridization or binding characteristics ofmultiple target substances (e.g., amplicons, primers, dNTPs, or anyother reagents and/or analytes) to multiple probes in real-time. Theprobes may be configured and/or designed such that one or more type oftarget substances may specifically bind or hybridize to one or moretypes of probes. As used herein, a probe “specifically binds” to aspecific target molecule if it binds to that molecule with greateraffinity than it binds to other substances in the sample. As providedelsewhere herein, certain types of probes may be contained within acertain percentage of independently addressable locations and uponbinding of target substances to the probes within the locations, signalsdetected or collected therefrom may be indicative or reflective of thepresence, amount, quantity, activity, and/or binding characteristics ofspecific types of substances.

The binding between the probes and the target substances may occur insolution (e.g., an aqueous solution). The binding between the targetsubstances and the probes and the signal detection can occurconcurrently or sequentially. For example, in some cases, the bindingbetween the probes and the target substances may occur prior to thedetection of the signals.

In some cases, the probe and the target substances may specifically bondto each other by hybridization. In some cases the binding can be throughother molecular recognition mechanisms. Molecular recognition mayinvolve detecting binding events between molecules. The strength ofbinding can be referred to as “affinity”. Affinities between biologicalmolecules may be influenced by non-covalent intermolecular interactions,for example, hydrogen bonding, hydrophobic interactions, electrostaticinteractions and Van der Waals forces. In multiplexed binding events, aplurality of target substances and probes may be involved. For example,in some cases, bindings between a plurality of different nucleic acidmolecules and/or different proteins may be tested. In such cases, it maybe preferred to have target substances preferentially bind to probes forwhich they have greater binding affinities. Thus, determining that aparticular probe is involved in a binding event may indicate thepresence of a target substance in the sample that has sufficientaffinity for the probe to meet the threshold level of detection of thedetection system being used. One may be able to determine the identityof the binding partner based on the specificity and strength of bindingbetween the probe and the substance.

The specific binding can be, for example, a receptor-ligand,enzyme-substrate, antibody-antigen, or a hybridization interaction. Theprobe/target substance binding pair can be nucleic acid to nucleic acid,e.g. DNA/DNA, DNA/RNA, RNA/DNA, RNA/RNA. The probe/target substancebinding pair can be a polypeptide and a nucleic acid, e.g.polypeptide/DNA and polypeptide/RNA, such as a sequence specific DNAbinding protein. The probe/target substance binding pair or can be anynucleic acid and synthetic DNA/RNA binding ligands (such as polyamides)capable of sequence-specific DNA or RNA recognition. The probe/targetsubstance binding pair can comprise natural binding compounds such asnatural enzymes and antibodies, and synthetic binding compounds. Theprobe/target substance binding can comprise aptamers, which are nucleicacid or polypeptide species that have been engineered to have specificbinding properties, usually through repeated rounds of in vitroselection or equivalently, SELEX (systematic evolution of ligands byexponential enrichment).

The hybridization or binding may result in a change in signal. Thesignal may be related to (e.g., proportional to) the amount ofhybridized or bound substances. For example, an assay where a 5 folddifference in concentration of the target substances may result in a 3to 6 fold difference in signal intensities. The signal may be related tothe binding affinities between the probes and the target substances. Thesignal intensity may be used to discriminate between different types oftarget substances. Control samples may or may not be tested and comparedto the target substances to be detected. In cases where more precisequantification is required, controls may be run to correct forvariations introduced in sample preparation and hybridization asdescribed herein.

Computer Control System

The present disclosure provides computer control system that isprogrammed to implement methods of the disclosure. FIG. 19 shows acomputer system 1901 that is programmed or otherwise configured toperform various functions of the methods and systems of the presentdisclosure, for example, performing an amplification reaction, real-timedetecting and/or monitoring the binding of target substances (e.g.,primers, amplicons) to an array of probes, identifying a threshold cycle(CO of an amplification reaction, and/or monitoring the progress of areaction. The computer system 1901 can regulate various aspects ofsimultaneously performing at least one amplification reaction anddetecting changes in signals produced by the probe array, such as, forexample, temperature control, reagent handling, and signal detection.The computer system 1901 can be intergraded with the systems provided inthe present disclosure.

The computer system 1901 includes a central processing unit (CPU, also“processor” and “computer processor” herein) 1905, which can be a singlecore or multi core processor, or a plurality of processors for parallelprocessing. The computer system 1901 also includes memory or memorylocation 1910 (e.g., random-access memory, read-only memory, flashmemory), electronic storage unit 1915 (e.g., hard disk), communicationinterface 1920 (e.g., network adapter) for communicating with one ormore other systems, and peripheral devices 1925, such as cache, othermemory, data storage and/or electronic display adapters. The memory1910, storage unit 1915, interface 1920 and peripheral devices 1925 arein communication with the CPU 1905 through a communication bus (solidlines), such as a motherboard. The storage unit 1915 can be a datastorage unit (or data repository) for storing data. The computer system1901 can be operatively coupled to a computer network (“network”) 1930with the aid of the communication interface 1920. The network 1930 canbe the Internet, an internet and/or extranet, or an intranet and/orextranet that is in communication with the Internet. The network 1930 insome cases is a telecommunication and/or data network. The network 1930can include one or more computer servers, which can enable distributedcomputing, such as cloud computing. The network 1930, in some cases withthe aid of the computer system 1901, can implement a peer-to-peernetwork, which may enable devices coupled to the computer system 1901 tobehave as a client or a server.

The CPU 1905 can execute a sequence of machine-readable instructions,which can be embodied in a program or software. The instructions may bestored in a memory location, such as the memory 1910. The instructionscan be directed to the CPU 1905, which can subsequently program orotherwise configure the CPU 1905 to implement methods of the presentdisclosure. Examples of operations performed by the CPU 1905 can includefetch, decode, execute, and writeback.

The CPU 1905 can be part of a circuit, such as an integrated circuit.One or more other components of the system 1901 can be included in thecircuit. In some cases, the circuit is an application specificintegrated circuit (ASIC).

The storage unit 1915 can store files, such as drivers, libraries andsaved programs. The storage unit 1915 can store user data, e.g., userpreferences and user programs. The computer system 1901 in some casescan include one or more additional data storage units that are externalto the computer system 1901, such as located on a remote server that isin communication with the computer system 1901 through an intranet orthe Internet.

The computer system 1901 can communicate with one or more remotecomputer systems through the network 1930. For instance, the computersystem 1901 can communicate with a remote computer system of a user(e.g., a lab technician, a physician). Examples of remote computersystems include personal computers (e.g., portable PC), slate or tabletPC's (e.g., Apple® iPad, Samsung® Galaxy Tab), telephones, Smart phones(e.g., Apple® iPhone, Android-enabled device, Blackberry®), or personaldigital assistants. The user can access the computer system 1901 via thenetwork 1930.

Methods as described herein can be implemented by way of machine (e.g.,computer processor) executable code stored on an electronic storagelocation of the computer system 1901, such as, for example, on thememory 1910 or electronic storage unit 1915. The machine executable ormachine readable code can be provided in the form of software. Duringuse, the code can be executed by the processor 1905. In some cases, thecode can be retrieved from the storage unit 1915 and stored on thememory 1910 for ready access by the processor 1905. In some situations,the electronic storage unit 1915 can be precluded, andmachine-executable instructions are stored on memory 1910.

The code can be pre-compiled and configured for use with a machine havea processer adapted to execute the code, or can be compiled duringruntime. The code can be supplied in a programming language that can beselected to enable the code to execute in a pre-compiled or as-compiledfashion.

Aspects of the systems and methods provided herein, such as the computersystem 1901, can be embodied in programming. Various aspects of thetechnology may be thought of as “products” or “articles of manufacture”typically in the form of machine (or processor) executable code and/orassociated data that is carried on or embodied in a type of machinereadable medium. Machine-executable code can be stored on an electronicstorage unit, such memory (e.g., read-only memory, random-access memory,flash memory) or a hard disk. “Storage” type media can include any orall of the tangible memory of the computers, processors or the like, orassociated modules thereof, such as various semiconductor memories, tapedrives, disk drives and the like, which may provide non-transitorystorage at any time for the software programming. All or portions of thesoftware may at times be communicated through the Internet or variousother telecommunication networks. Such communications, for example, mayenable loading of the software from one computer or processor intoanother, for example, from a management server or host computer into thecomputer platform of an application server. Thus, another type of mediathat may bear the software elements includes optical, electrical andelectromagnetic waves, such as used across physical interfaces betweenlocal devices, through wired and optical landline networks and overvarious air-links. The physical elements that carry such waves, such aswired or wireless links, optical links or the like, also may beconsidered as media bearing the software. As used herein, unlessrestricted to non-transitory, tangible “storage” media, terms such ascomputer or machine “readable medium” refer to any medium thatparticipates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, maytake many forms, including but not limited to, a tangible storagemedium, a carrier wave medium or physical transmission medium.Non-volatile storage media include, for example, optical or magneticdisks, such as any of the storage devices in any computer(s) or thelike, such as may be used to implement the databases, etc. shown in thedrawings. Volatile storage media include dynamic memory, such as mainmemory of such a computer platform. Tangible transmission media includecoaxial cables; copper wire and fiber optics, including the wires thatcomprise a bus within a computer system. Carrier-wave transmission mediamay take the form of electric or electromagnetic signals, or acoustic orlight waves such as those generated during radio frequency (RF) andinfrared (IR) data communications. Common forms of computer-readablemedia therefore include for example: a floppy disk, a flexible disk,hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD orDVD-ROM, any other optical medium, punch cards paper tape, any otherphysical storage medium with patterns of holes, a RAM, a ROM, a PROM andEPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wavetransporting data or instructions, cables or links transporting such acarrier wave, or any other medium from which a computer may readprogramming code and/or data. Many of these forms of computer readablemedia may be involved in carrying one or more sequences of one or moreinstructions to a processor for execution.

The computer system 1901 can include or be in communication with anelectronic display 1935 that comprises a user interface (UI) 1940 forproviding, for example, cycle numbers, temperature values, temperaturecontrol, detector data, and reagent handling. Examples of UI's include,without limitation, a graphical user interface (GUI) and web-based userinterface. Methods and systems of the present disclosure can beimplemented by way of one or more algorithms. An algorithm can beimplemented by way of software upon execution by the central processingunit 1905. The algorithm can, for example, control the temperatures ofeach of the addressable locations, collect signals and analyze collecteddata.

EXAMPLES Example 1: Threshold Cycle (C_(t)) Identification

Threshold cycle (C_(t)), the intersection between an amplification curveand a threshold line and a relative measure of the concentration of atarget substance in an amplification reaction, can be measured with themethods, devices and systems of the present disclosure. The left andright two plots in FIGS. 9A-9D illustrate the determination of C_(t) inan example asymmetric amplification reaction and a conventionalamplification reaction respectively. In asymmetric amplificationreaction (FIGS. 9A and 9B), a limiting primer is utilized, i.e., theconcentration of the limiting primer is much lower than theconcentration of the other primer of the primer pair. Both primers ofthe primer pair may be labeled with reporter molecules (e.g., energyacceptors). As the amplification reaction proceeds, both primers in theprimer pair are consumed. Due to its lower starting concentration, thelimiting primer is depleted much faster than its counterpart. Some ofthe probes may be designed to specifically bind to the limiting primersand the signal change upon the binding between the probes and thelimiting primers is indicative of the progress of the amplificationreaction. As FIG. 9B shows, at the early stage of the amplification,only a few limiting primers (i.e., P(+)) participate in theamplification reaction and the binding/hybridization between thelimiting primer and the probe produces little to no signals. With theprogress of the amplification reaction, more and more limiting primerstake part in the amplification reaction and less binding pairs (i.e.,limiting primer and probe) may be found in the reaction mixture. Thedecrease in the number of binding pairs result in an increase of signalsfrom the probes, and a plateau may be soon reached as the limitingprimers are depleted. According to the signal change with cycle numbers,a threshold cycle (CO can easily be identified.

On the other hand, in a conventional amplification method (FIGS. 9C and9D), a pair of primers with substantially the same concentration isutilized for amplifying the target nucleic acid sequences. In suchmethod, a donor-labeled probe is applied. Such labeled probe mayemit/generate signals prior to its binding to an amplified product. Atthe early stage of the amplification reaction, very few amplicons areproduced and signals produced by the probes are less influenced. Theamplicons then accumulate exponentially with the number of thermalcycles and bind to numerous probes. This binding between the ampliconsand the probes result in a drop of signals produced by the probes. Byplotting the signals with the cycle numbers, a threshold cycle (CO canbe determined.

Example 2: Primer Depletion Method to Detect on-Chip AmplificationReaction

FIGS. 14A-14C shows an example primer depletion method of detecting anon-chip amplification reaction. As FIG. 14A shows, a probe array havinga plurality of probes is provided. Each of the probes is labeled with areporter molecule (e.g., an energy donor) and configured to be capableof binding to a limiting primer in a primer pair. The limiting primersmay be labeled with another type of reporter molecules such that uponbinding of the primers to the probes, the signals initially produced bythe probes may be reduced or eliminated. As the amplification reactionproceeds, more and more limiting primers are consumed and less bindingpairs may exist, which therefore causes an increase of signals detectedfrom the probe array. As will be appreciated, the total intensities ofsignals detected or obtained from the probe array may be highlydependent on the number of thermal cycles. By using a thermal controlmodule, temperature profiles of can be precisely controlled, as shown inFIG. 14C. Progress of the amplification reaction may then be monitoredin real-time by detecting the total signal intensities of the probes(FIG. 14B).

FIGS. 15-18 show example data obtained by a primer depletion method ofthe present disclosure. As illustrated in FIG. 15, at least two kinds ofprobes are utilized, each of which can specifically bind to a primersequence and a control sequence. The control sequence is designed insuch a way that it does not participate in the amplification reactionthus the signals produced by control sequence-probe binding pair isindependent of the progress of the amplification reaction.

FIG. 16 shows the time dependence of fluorescence detected andtemperature of the amplification reaction. As shown in FIG. 16, adecrease of fluorescent signal detected for the control sequences is dueto the photobleaching. While for primer sequences, an increase in timeconstant τ is observed, which may be due to the lowering of primerconcentrations. By plotting the measured time constant τ against thecycle number, the progress of the amplification reaction can bemonitored.

With methods and systems provided herein, the amplification reaction canbe monitored in real-time (FIG. 17) and a correlation or associationbetween threshold cycle (CO and template concentration can be identified(FIG. 18).

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. It is not intendedthat the invention be limited by the specific examples provided withinthe specification. While the invention has been described with referenceto the aforementioned specification, the descriptions and illustrationsof the embodiments herein are not meant to be construed in a limitingsense. Numerous variations, changes, and substitutions will now occur tothose skilled in the art without departing from the invention.Furthermore, it shall be understood that all aspects of the inventionare not limited to the specific depictions, configurations or relativeproportions set forth herein which depend upon a variety of conditionsand variables. It should be understood that various alternatives to theembodiments of the invention described herein may be employed inpracticing the invention. It is therefore contemplated that theinvention shall also cover any such alternatives, modifications,variations or equivalents. It is intended that the following claimsdefine the scope of the invention and that methods and structures withinthe scope of these claims and their equivalents be covered thereby.

1.-30. (canceled)
 31. A method for assaying at least one templatenucleic acid molecule, comprising: (a) activating a sensor arraycomprising (i) a substrate comprising a plurality of first probesimmobilized to a first addressable location, a plurality of secondprobes immobilized to a second addressable location, wherein said firstprobes are capable of capturing an individual primer of a primer set,and wherein said second probes are capable of capturing a controlnucleic acid molecule, and (ii) an array of detectors configured todetect at least one first signal from said first addressable locationand at least one second signal from said second addressable location,wherein a difference between said at least one first signal and said atleast one second signal over time is indicative of said individualprimer binding with an individual probe of said plurality of firstprobes; (b) subjecting a reaction mixture to a nucleic acidamplification reaction under conditions sufficient to yield at least onetarget nucleic acid molecule as an amplification product(s) of saidtemplate nucleic acid molecule, wherein said reaction mixture comprises(i) a nucleic acid sample containing or suspected of containing saidtemplate nucleic acid molecule, (ii) said primer set, (iii) said controlnucleic acid molecule, and (iv) a polymerizing enzyme, wherein saidindividual primer of said primer set has sequence complementarity withsaid template nucleic acid molecule; (c) using said array of detectorsto detect said at least one first signal and said at least one secondsignal at multiple time points during said nucleic acid amplificationreaction; and (d) using said difference between said at least one firstsignal and said at least one second signal to detect said templatenucleic acid molecule.
 32. The method of claim 31, wherein said at leastone first signal is produced upon binding of said individual probe tosaid individual primer, and wherein said at least one second signal isproduced upon binding of an additional probe of said second probes tosaid control nucleic acid molecule.
 33. The method of claim 31, whereinsaid control nucleic acid molecule is not amplified in saidamplification reaction.
 34. The method of claim 31, wherein saiddifference is between a first time constant of said at least one firstsignal and a second time constant of said at least one second signal.35. The method of claim 31, wherein said reaction mixture comprises aplurality of template nucleic acid molecules, and wherein said firstprobes specifically bind to a plurality of target nucleic molecules asamplification products of said plurality of said template nucleic acidmolecules.
 36. The method of claim 31, wherein said primer set comprisesa plurality of individual primers having different nucleic acidsequences, and wherein said first probes are configured to specificallybind to said plurality of said individual primers.
 37. The method ofclaim 31, wherein said reaction mixture is provided in a reactionchamber configured to retain said reaction mixture and permit said firstand second probes to bind to said individual primer and said controlnucleic acid molecule.
 38. The method of claim 31, further comprisingcorrelating said at least one first signal detected at multiple timepoints with an initial concentration of said at least one templatenucleic acid molecule by analyzing a binding rate of said probes withsaid individual primer from said primer set.
 39. The method of claim 31,wherein said first probes or said second probes are oligonucleotides.41. The method of claim 31, wherein said sensor array comprises at leastabout 100 integrated sensors.
 42. The method of claim 31, wherein saidat least one first signal is a first optical signal that is indicativeof a first interaction between a first energy acceptor and a firstenergy donor associated with said individual primer and said individualprobe, and wherein said at least one second signal is a second opticalsignal that is indicative of a second interaction between a secondenergy acceptor and a second energy donor associated with said controlnucleic acid molecule and an additional probe of said second probes. 43.The method of claim 42, wherein said first energy acceptor is coupled tosaid individual primer, and wherein said second energy acceptor iscoupled to said control nucleic acid molecule.
 44. The method of claim42, wherein said first energy acceptor is coupled to said target nucleicacid molecule.
 45. The method of claim 42, wherein said first energyacceptor is a first quencher, and wherein said second energy acceptor isa second quencher.
 46. The method of claim 42, wherein said first energydonor is a first fluorophore, and wherein said second energy donor is asecond fluorophore.
 47. The method of claim 42, wherein said firstenergy donor is coupled to said first probe, and wherein said secondenergy donor is coupled to said second probe.
 48. The method of claim31, wherein said target nucleic acid molecule is detected at asensitivity of at least about 90%.
 49. The method of claim 31, whereinsaid at least one first signal is detected while said reaction mixturecomprising said target nucleic acid molecule is in fluid contact withsaid sensor array.
 50. A system for assaying at least one templatenucleic acid molecule, comprising: (a) a reaction chamber comprising areaction mixture, wherein said reaction mixture comprises (i) a nucleicacid sample containing or suspected of containing said template nucleicacid molecule, (ii) a primer set comprising an individual primer, (iii)a control nucleic acid molecule, and (iv) a polymerizing enzyme, whereinsaid individual primer of said primer set has sequence complementaritywith said template nucleic acid molecule, wherein said reaction chambercomprising said reaction mixture is configured to facilitate a nucleicacid amplification reaction with said reaction mixture under conditionssufficient to yield at least one target nucleic acid molecule as anamplification product(s) of said template nucleic acid molecule, whereinsaid nucleic acid amplification reaction does not yield anyamplification product of said control nucleic acid; (b) a sensor arraycomprising (i) a substrate comprising a plurality of first probesimmobilized to a first addressable location, a plurality of secondprobes immobilized to a second addressable location, wherein said firstprobes are capable of capturing said individual primer of said primerset, and wherein said second probes are capable of capturing saidcontrol nucleic acid molecule, and (ii) an array of detectors configuredto detect at least one first signal from said first addressable locationand at least one second signal from said second addressable location,wherein a difference between said at least one first signal and said atleast one second signal over time is indicative of said individualprimer binding with an individual probe of said plurality of firstprobes; and (c) a computer processor coupled to said sensor array andprogrammed to (i) subject said reaction mixture to said nucleic acidamplification reaction, and (ii) detect said at least one first signaland said at least one second signal at multiple time points during saidnucleic acid amplification reaction.